Automatic MD equilibration and diffusion coefficient convergence for glycine in water¶
This examples shows how to iteratively expand equilibration and production molecular dynamics simulations until some monitored properties (energy, temperature, diffusion coefficient) are converged.
Requires: AMS2026 or later
Related documentation
Related examples
Related tutorials
Packed glycine-water periodic system.
Result¶
The final glycine center-of-mass diffusion coefficient is 1.511364e-09 m^2/s with a fitted MSD R^2 of 0.997441. The MSD correlation window is 20 ps and the fitted interval is 5-20 ps. The cumulative production trajectory is 300 ps. The last three cumulative estimates are each within 15% of their mean, so the production estimate is converged by the specified test.
The mean of the final three cumulative estimates is 1.362155e-09 m^2/s. This mean is used only for the convergence test; the reported coefficient comes from the full 300 ps trajectory.
The production trajectory has a mean temperature of 380.189 +/- 27.099 K and a mean pressure of 3.452129e+08 +/- 6.113907e+08 Pa. The fragmentation or atom-exchange status is not detected.
System and protocol¶
The periodic cubic starting system contains one neutral NH2-CH2-COOH glycine molecule and 40 water molecules. It has 130 atoms and an initial packed density of 1.000000 g/cm^3. ReaxFF used Glycine.ff with nproc=1. The geometry optimization used Basic convergence. Equilibration used Berendsen NVT at 380 K with a 100 fs coupling time. Production used a separate NHC NVT trajectory with a 100 fs coupling time. Both MD stages used a 0.5 fs timestep and stored a frame every 100 fs.
The equilibration endpoint is 45 ps and its convergence status is accepted.
Equilibration convergence¶
duration_ps |
window_start_ps |
window_end_ps |
fitted_energy_change_hartree |
energy_std_hartree |
abs_change_over_std |
mean_temperature_k |
temperature_error_percent |
energy_pass |
temperature_pass |
combined_pass |
consecutive_passes |
accepted |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
10 |
5 |
10 |
-0.0190687 |
0.0164304 |
1.16057 |
380.343 |
0.0902924 |
False |
True |
False |
0 |
False |
15 |
7.5 |
15 |
0.00287543 |
0.0168213 |
0.17094 |
383.242 |
0.853122 |
True |
True |
True |
1 |
False |
20 |
10 |
20 |
0.0114965 |
0.0170214 |
0.675412 |
380.281 |
0.0738878 |
False |
True |
False |
0 |
False |
25 |
12.5 |
25 |
0.000842544 |
0.0156176 |
0.0539484 |
379.496 |
0.132534 |
True |
True |
True |
1 |
False |
30 |
15 |
30 |
-0.0112081 |
0.0155284 |
0.721783 |
377.881 |
0.557719 |
False |
True |
False |
0 |
False |
35 |
17.5 |
35 |
-0.0111003 |
0.0153148 |
0.724808 |
378.855 |
0.301305 |
False |
True |
False |
0 |
False |
40 |
20 |
40 |
-0.00480942 |
0.0145039 |
0.331594 |
380.175 |
0.0461648 |
True |
True |
True |
1 |
False |
45 |
22.5 |
45 |
0.00470817 |
0.0153053 |
0.307618 |
380.689 |
0.181303 |
True |
True |
True |
2 |
True |
The energy test fits the five block-mean potential energies over the trailing half of each accumulated trajectory. It passes when the fitted change is no more than 0.5 times the trajectory standard deviation. The temperature test requires the trailing mean to lie within 2% of 380 K. Two consecutive combined passes are required.
Production convergence¶
duration_ps |
diffusion_m2_s |
last_three_mean_m2_s |
last_three_max_deviation_percent |
converged |
|---|---|---|---|---|
100 |
1.03978e-09 |
nan |
nan |
False |
150 |
9.95771e-10 |
nan |
nan |
False |
200 |
1.36014e-09 |
1.1319e-09 |
20.1646 |
False |
250 |
1.21496e-09 |
1.19029e-09 |
16.3422 |
False |
300 |
1.51136e-09 |
1.36216e-09 |
10.9539 |
True |
CSV data are in `tables/ <tables/>`__. The convergence histories, thermodynamic traces, and MSD values shown here come directly from the individual AMS and Analysis job directories.
Limitations¶
The box contains only 40 water molecules. Periodic hydrodynamic finite-size effects can therefore bias the diffusion coefficient. No finite-size correction or independent replicate trajectories were applied. The fixed-density NVT state also prevents density relaxation and makes the reported mean pressure an observation rather than a controlled state variable.
Complete calculation inputs¶
Initial ReaxFF geometry optimization¶
Provenance: /home/ubuntu/work/01-initial-system_workdir/setup_opt
GeometryOptimization
Convergence
Quality Basic
End
End
Task GeometryOptimization
System
Atoms
N 1.2281940000 7.1738140000 7.3324350000 region=glycine
C 2.5627490000 7.3379360000 7.8363910000 region=glycine
C 2.6378550000 7.5441720000 9.2925960000 region=glycine
O 1.6426130000 7.4817520000 10.0719620000 region=glycine
O 3.8740130000 7.9426300000 9.8084330000 region=glycine
H 1.2580100000 7.3712460000 6.3017280000 region=glycine
H 0.9461930000 6.1688350000 7.4105530000 region=glycine
H 3.0316870000 8.1755850000 7.2622640000 region=glycine
H 3.1888220000 6.4463850000 7.5799160000 region=glycine
H 4.7592150000 7.6221990000 9.4594070000 region=glycine
O 2.8743300000 4.8500010000 5.4275130000 region=water
H 3.7118750000 5.3221630000 5.2365690000 region=water
H 2.1693960000 5.4632870000 5.7294450000 region=water
O 9.5338540000 4.9835590000 9.8024440000 region=water
H 9.9680140000 4.4902400000 9.0751060000 region=water
H 9.9735900000 5.8446590000 9.9737720000 region=water
O 4.2904420000 1.1762610000 9.9876590000 region=water
H 3.4023330000 0.9942730000 9.6148020000 region=water
H 5.0047950000 0.9814380000 9.3427110000 region=water
O 4.2805610000 2.3894080000 5.7250290000 region=water
H 3.5480290000 2.8887250000 6.1433090000 region=water
H 4.9137390000 2.9840080000 5.2670440000 region=water
O 3.1201750000 4.2431350000 3.3282950000 region=water
H 2.1677470000 4.4685780000 3.3824840000 region=water
H 3.2687430000 3.2730100000 3.3599170000 region=water
O 1.0350490000 1.0933760000 3.7970630000 region=water
H 1.1849970000 2.0222430000 3.5221080000 region=water
H 1.0032430000 1.0018090000 4.7742110000 region=water
O 1.7588500000 2.5525240000 9.4261730000 region=water
H 1.9241970000 3.3640490000 9.9505460000 region=water
H 1.3032860000 1.8618730000 9.9550190000 region=water
O 3.7777050000 9.4109060000 5.6032650000 region=water
H 4.5727600000 9.9835680000 5.6319810000 region=water
H 2.9480700000 9.9359880000 5.6177340000 region=water
O 9.3199090000 8.2892990000 3.1125280000 region=water
H 8.9793070000 7.5576830000 2.5561040000 region=water
H 8.6037300000 8.9002450000 3.3919000000 region=water
O 9.5978570000 9.1395960000 8.3427440000 region=water
H 9.8069050000 8.1820350000 8.3267630000 region=water
H 9.1668250000 9.4337620000 7.5109440000 region=water
O 6.8855070000 3.9843750000 3.9838930000 region=water
H 7.5338410000 3.7983390000 3.2726030000 region=water
H 5.9652130000 4.0098670000 3.6423920000 region=water
O 3.4688030000 5.1630140000 10.0021910000 region=water
H 2.7002820000 5.3537330000 9.4243660000 region=water
H 4.3082360000 5.4949840000 9.6157170000 region=water
O 6.8937070000 7.6877530000 1.7415270000 region=water
H 7.4386890000 7.3504620000 0.9998340000 region=water
H 6.0009320000 7.9662860000 1.4422150000 region=water
O 1.7598440000 0.9837060000 7.1327360000 region=water
H 1.4321260000 1.8795720000 7.3583550000 region=water
H 2.4476560000 1.0115050000 6.4324810000 region=water
O 4.1997220000 3.4776740000 8.7527800000 region=water
H 4.6084860000 3.3218650000 9.6300000000 region=water
H 4.0288850000 2.6372980000 8.2744510000 region=water
O 3.1328560000 10.0060880000 8.7831480000 region=water
H 3.0323260000 9.9747400000 9.7577200000 region=water
H 4.0216830000 9.7020520000 8.4972050000 region=water
O 7.6429470000 6.4648490000 9.9754570000 region=water
H 8.2659810000 7.2216230000 9.9761680000 region=water
H 6.7069550000 6.7617160000 9.9739300000 region=water
O 1.1238710000 7.3330540000 3.5435330000 region=water
H 1.7100530000 6.6146260000 3.8615420000 region=water
H 0.9950830000 8.0284910000 4.2247060000 region=water
O 3.1711510000 9.4228500000 3.4904940000 region=water
H 3.9847110000 9.9696440000 3.4868070000 region=water
H 2.3593370000 9.9751680000 3.5013810000 region=water
O 3.4498030000 7.8083110000 1.4650990000 region=water
H 3.8632030000 7.0535670000 0.9956940000 region=water
H 2.8233570000 7.5084470000 2.1592620000 region=water
O 9.9723070000 3.2471620000 4.1010420000 region=water
H 9.7026170000 4.0052240000 3.5411420000 region=water
H 9.7762750000 2.3866170000 3.6706370000 region=water
O 1.1847490000 9.2145870000 8.1480430000 region=water
H 0.9941810000 9.5632080000 9.0441610000 region=water
H 0.9987840000 9.8794660000 7.4497820000 region=water
O 5.5152160000 2.1951010000 1.8362650000 region=water
H 6.0909770000 2.0777250000 2.6208670000 region=water
H 6.0269930000 2.1622210000 0.9988770000 region=water
O 4.2847400000 7.4837140000 4.6872470000 region=water
H 5.1608280000 7.9146060000 4.7748920000 region=water
H 4.1840880000 7.0325960000 3.8208890000 region=water
O 7.4123570000 4.0310040000 6.3218290000 region=water
H 6.5495100000 3.6288330000 6.5555640000 region=water
H 7.3388210000 5.0005640000 6.1848560000 region=water
O 5.7067250000 4.8279570000 0.9995700000 region=water
H 5.1071620000 4.7922320000 1.7742490000 region=water
H 6.6347100000 4.6216190000 1.2455040000 region=water
O 5.2963200000 5.5925530000 6.7352960000 region=water
H 5.2311150000 6.5689220000 6.7929970000 region=water
H 4.9476720000 5.1544260000 7.5419580000 region=water
O 6.2306090000 6.2425450000 3.6556510000 region=water
H 6.1664930000 5.9676770000 4.5943820000 region=water
H 7.1497980000 6.1753050000 3.3168510000 region=water
O 2.4362630000 4.3326510000 0.9611220000 region=water
H 2.8296630000 5.1439010000 1.3458130000 region=water
H 2.9471600000 3.5291710000 1.2011620000 region=water
O 6.7782980000 1.7758440000 8.3161120000 region=water
H 7.1350590000 0.9981570000 8.7944460000 region=water
H 7.4593280000 2.4720120000 8.1905540000 region=water
O 4.0403210000 1.2242650000 3.1486030000 region=water
H 4.3717030000 0.9820800000 4.0387770000 region=water
H 3.0945060000 0.9868340000 3.0333770000 region=water
O 9.9753760000 5.9936110000 4.5959620000 region=water
H 9.0696320000 6.3021160000 4.3830490000 region=water
H 9.9719860000 5.3041600000 5.2951470000 region=water
O 6.5718080000 9.3078860000 6.1595700000 region=water
H 6.9689030000 9.9751830000 6.7578240000 region=water
H 6.8836870000 9.4143460000 5.2345770000 region=water
O 9.5890600000 2.3236390000 9.6084840000 region=water
H 8.8423730000 2.8441540000 9.9723540000 region=water
H 9.2874010000 1.4737850000 9.2199420000 region=water
O 8.8977610000 2.2830250000 6.5417060000 region=water
H 9.4518700000 3.0631070000 6.7545790000 region=water
H 8.6982760000 2.2270900000 5.5818660000 region=water
O 8.7041910000 2.3434330000 1.2535510000 region=water
H 9.1466590000 3.1496010000 1.5929530000 region=water
H 9.3516940000 1.6503050000 0.9995270000 region=water
O 1.5713830000 4.0989480000 7.8049630000 region=water
H 2.5122130000 4.2112950000 7.5537730000 region=water
H 0.9911510000 4.0076630000 7.0180630000 region=water
O 7.2924750000 7.6521450000 8.0508440000 region=water
H 6.5943890000 8.2828490000 8.3261020000 region=water
H 7.2286710000 7.4295900000 7.0965830000 region=water
O 7.2240600000 4.2529950000 9.4589840000 region=water
H 6.5947550000 4.8138900000 8.9587330000 region=water
H 6.7625820000 3.5579990000 9.9768950000 region=water
O 9.1683180000 5.7433810000 7.4569070000 region=water
H 8.3489470000 5.7251700000 7.9946610000 region=water
H 9.2466430000 6.5731420000 6.9376990000 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 5 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_005ps
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
InitialVelocities
Temperature 380.0
Type Random
End
NSteps 10000
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 1.3482433945 7.1933736074 7.2825879312 region=glycine
C 2.7432713754 7.5023634327 7.7575110950 region=glycine
C 2.8365986194 7.7589518236 9.2741683520 region=glycine
O 1.8746954418 8.0240812926 9.9247898874 region=glycine
O 4.1174562420 7.7611240843 9.8194363666 region=glycine
H 1.2813659396 7.1640118916 6.2631253604 region=glycine
H 1.0280970197 6.2558918755 7.5816979078 region=glycine
H 3.1187686566 8.4152625655 7.1735509973 region=glycine
H 3.3879753123 6.6436741148 7.4558438321 region=glycine
H 4.6556940492 7.6097369324 8.9955912555 region=glycine
O 2.7175951668 4.9630258436 5.1423395010 region=water
H 3.4333355935 5.6207939739 5.3223231106 region=water
H 2.2335750662 4.8301479402 5.9972324189 region=water
O 10.0433002022 4.9267499529 10.2481504640 region=water
H 10.3161733871 5.1461512101 9.3593903348 region=water
H 9.2108291708 5.4013551420 10.3271471342 region=water
O 4.8055139039 1.7216141013 9.9364737017 region=water
H 4.1054818113 1.0074413397 9.7831100348 region=water
H 5.6400679047 1.3790991470 9.4576572308 region=water
O 4.5855160614 2.4867357891 5.6134097054 region=water
H 3.9968917174 3.2562245443 5.4924859259 region=water
H 5.4152499765 2.7828990779 5.1718150277 region=water
O 3.8384979254 4.0109415177 2.8039249673 region=water
H 3.4169452437 4.3692789325 3.6231846096 region=water
H 3.9246882561 2.9999025011 2.9446936666 region=water
O 1.2227729859 1.1071958565 4.1046707360 region=water
H 0.5697189005 1.7990443326 3.8598786187 region=water
H 1.3302454144 1.1966981566 5.0754937776 region=water
O 1.2417768262 2.1428225427 9.7355640571 region=water
H 1.4742704719 2.5086844993 10.6042523688 region=water
H 0.2673152706 1.9793984299 9.7590616004 region=water
O 3.6651769497 9.9752499618 6.2924367070 region=water
H 4.6213413436 9.8313408792 6.1350948660 region=water
H 3.2253185988 9.7576402956 5.4162565047 region=water
O 9.0070436177 8.2980951037 3.4247888386 region=water
H 9.6237182146 8.1021724258 2.7182921002 region=water
H 8.1497849567 8.3187303214 2.9660997621 region=water
O 9.0022870595 8.7681105380 8.2785209820 region=water
H 9.9679985667 8.8688653439 8.2740519691 region=water
H 8.7265233157 9.6403356603 7.9857378795 region=water
O 6.6259062387 3.2827919746 3.7925032772 region=water
H 7.1074860347 2.8735008379 3.0678634757 region=water
H 5.9681665056 3.7965046280 3.3176501229 region=water
O 2.8354319921 4.9696298790 10.3104966013 region=water
H 2.4909076414 4.6648716858 9.4733046101 region=water
H 3.7409883287 5.1831355388 10.0899058417 region=water
O 6.7423777913 8.4385279151 1.5434309480 region=water
H 7.1800440359 7.9162021193 0.8368988422 region=water
H 5.8595810182 8.0492320254 1.6554173820 region=water
O 1.8217549328 1.5187192485 6.8935013216 region=water
H 1.8526082005 1.6490568343 7.8536747992 region=water
H 2.7390299082 1.3432181716 6.6690560225 region=water
O 4.1968582856 3.6112197439 8.1697547875 region=water
H 4.3262143498 3.0077863767 8.9730867716 region=water
H 4.4142673832 3.0561900967 7.3969304618 region=water
O 3.2914924758 10.6913796602 9.0413825439 region=water
H 3.3913963780 9.8544125607 9.5068703754 region=water
H 3.5510672390 10.4934769801 8.1224366365 region=water
O 8.0444648209 7.1231753810 10.4056132151 region=water
H 8.5253218825 7.8061688060 9.9077743822 region=water
H 7.3505322101 6.8462004104 9.7999099221 region=water
O 1.6334725326 7.1318079621 3.2243983355 region=water
H 2.0676721973 6.6086791244 3.9142411776 region=water
H 1.8094099854 8.0531085465 3.4789959248 region=water
O 2.6573725274 9.7321509480 3.7858961790 region=water
H 3.3510817538 10.2801766230 3.3863506732 region=water
H 1.9050595424 10.3524156537 3.8576062359 region=water
O 3.9473591331 7.4410297304 1.7573373702 region=water
H 3.7993530372 7.5369249147 0.8048635076 region=water
H 3.0512724236 7.2718922496 2.1376737555 region=water
O 10.1857546009 3.0177527630 4.1040457642 region=water
H 10.0197211445 3.9542801225 4.3189778301 region=water
H 9.7801096557 2.8907724840 3.2181768583 region=water
O 0.4407691610 10.0467538449 7.7182514162 region=water
H 0.9962343135 9.3137426657 7.9855204896 region=water
H 1.0557503247 10.7766808652 7.5813221002 region=water
O 5.9621390329 2.0952665762 1.4478166938 region=water
H 5.3562823311 1.9449003334 2.1932786508 region=water
H 5.4163753607 1.9421822991 0.6436596654 region=water
O 4.0842864618 7.3422481208 4.8717977717 region=water
H 5.0112626466 7.5593685350 4.9758932378 region=water
H 3.9795900317 7.4323213775 3.9231022481 region=water
O 7.1214205493 3.5192211020 7.0477676855 region=water
H 6.2254146695 3.5124341915 6.6856020697 region=water
H 7.3884256085 4.4167355901 6.8129520810 region=water
O 5.7816382522 4.7646071931 0.9577622246 region=water
H 5.0922203615 5.0989972503 1.5524093829 region=water
H 5.9502457210 3.8355916323 1.2682266520 region=water
O 5.3188597972 5.4025490990 6.3474716708 region=water
H 5.4801194310 6.3049655780 6.6631558859 region=water
H 4.9593774357 4.9252837075 7.1226191783 region=water
O 6.7097187967 6.3617931999 3.9847866465 region=water
H 6.2070854522 5.8776128516 4.6526056429 region=water
H 7.6334515824 6.0409203753 4.0531268176 region=water
O 1.7006732139 3.5132916247 1.2777129156 region=water
H 1.8079973321 4.1878380385 0.5696500340 region=water
H 2.4300931953 3.7282008750 1.9408651815 region=water
O 6.9266347866 0.8719436332 8.5105140057 region=water
H 7.6902211141 1.0322322101 9.0927737898 region=water
H 6.9716870124 1.6336564074 7.9122002070 region=water
O 3.8198087581 1.3873775969 3.2876114084 region=water
H 4.1919538908 1.5381251717 4.2094882642 region=water
H 2.8284068743 1.3267386725 3.4135114002 region=water
O 9.3581063686 5.7550823097 4.5409584399 region=water
H 9.4250389923 6.6745946454 4.1895931695 region=water
H 9.3739279237 5.8360980618 5.5194415475 region=water
O 6.4141630106 9.5171505643 5.7853374231 region=water
H 6.7865028806 10.2402525523 6.2915498274 region=water
H 7.0946603466 9.3722557560 5.1276920888 region=water
O 9.4904045942 1.8060314024 9.5886840853 region=water
H 9.1209585966 2.7061278958 9.6943354965 region=water
H 9.6210396612 1.7181246862 8.6191794448 region=water
O 9.5524202357 2.0064989195 6.7550917550 region=water
H 8.6731159291 2.4033975239 6.6731406190 region=water
H 9.9990406844 2.2441334141 5.9308191575 region=water
O 9.2080589431 2.7754060335 1.4475982879 region=water
H 9.4364205764 3.5073479180 0.8673693423 region=water
H 9.2503552288 2.0425343529 0.8344589090 region=water
O 1.4560043528 4.3322934490 7.5261158871 region=water
H 2.3341796474 3.9942770598 7.7928914672 region=water
H 0.9999960026 3.5142385117 7.2718611218 region=water
O 6.1833343525 7.5976729493 7.8923754927 region=water
H 7.0207511492 7.8043837451 8.3310480725 region=water
H 6.1588539970 8.2483691277 7.1630835144 region=water
O 7.4663508388 3.9410713824 9.6838202121 region=water
H 6.9948997708 3.6894833732 8.8655559377 region=water
H 6.7873742435 4.1229910377 10.3481293489 region=water
O 9.1680836121 5.8585453044 7.3877689735 region=water
H 8.5956916508 5.3515787859 7.9671346593 region=water
H 9.0539887958 6.7620706429 7.7000117621 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 10 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_010ps
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_005ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 20000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_005ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 4.6694817673 4.4382242179 9.1209929138 region=glycine
C 5.2927837313 5.8318224333 9.1635611385 region=glycine
C 4.8582260597 6.8107612168 10.2808212578 region=glycine
O 4.5716111299 6.4682367410 0.4024492826 region=glycine
O 5.3122724729 8.1541812953 10.0517910437 region=glycine
H 4.7935746200 4.0255649383 8.1231082087 region=glycine
H 5.2197031650 3.7522367487 9.7237522662 region=glycine
H 4.9912366237 6.2568904897 8.1689840732 region=glycine
H 6.4418520652 5.7248768675 9.0578857765 region=glycine
H 5.1052368978 8.2204225890 9.1219837639 region=glycine
O 7.1338406900 8.2812728733 3.2921588005 region=water
H 7.4828162991 7.5470149600 3.8319922898 region=water
H 6.6084695560 8.8469719932 3.8157826856 region=water
O 10.6645294568 2.3644221720 7.5740591978 region=water
H 0.4642831260 1.9553881148 7.3103747279 region=water
H 10.3867753329 1.7523158636 8.2922497915 region=water
O 3.7653514742 1.2391848005 2.0495672009 region=water
H 2.8770138701 0.9547469682 1.9432174330 region=water
H 3.7972812566 1.7946894383 2.8543990431 region=water
O 2.0748089742 8.9021389344 4.8341056331 region=water
H 2.6425407006 8.0966442282 4.8161977714 region=water
H 2.6646916325 9.5693806611 5.1805835689 region=water
O 1.6976848093 3.7776437761 1.5090056353 region=water
H 1.6586987506 3.6527813381 0.5640180226 region=water
H 1.1966600908 4.5584599387 1.7217208980 region=water
O 0.1593426578 4.1125292260 4.3090250318 region=water
H 10.6528316652 4.9233457473 4.3273699227 region=water
H 0.9601848049 4.3967618584 4.8518157601 region=water
O 4.9633576666 2.9215802034 6.6896581350 region=water
H 5.8820571426 2.8679621463 6.3365460027 region=water
H 4.8264628714 2.0283136781 6.7165565678 region=water
O 10.7157513939 5.6617775319 1.0260253912 region=water
H 10.6600695891 5.6850865169 0.0236035170 region=water
H 10.9527607418 6.5673745787 1.3132356946 region=water
O 5.0684135303 3.7990339439 3.9749060984 region=water
H 4.9879161863 3.2813622953 4.7844345896 region=water
H 4.4646830353 3.4303190599 3.3158120057 region=water
O 5.3309915710 7.7414704646 6.8781976348 region=water
H 4.4913157906 7.9026228087 6.4605540432 region=water
H 6.0490344515 7.7680697997 6.2505421865 region=water
O 1.1157495109 0.1574676414 1.2703635949 region=water
H 0.8590459620 0.3250305126 2.2031705035 region=water
H 0.4657331787 0.5824480443 0.6851357522 region=water
O 8.4247459540 1.9318872882 4.8164183309 region=water
H 9.2582461283 1.5245650675 4.8802121219 region=water
H 8.5456005249 2.6069207147 4.1279859540 region=water
O 8.1187920961 1.0570928202 0.3053202949 region=water
H 7.4541025407 1.4177238520 10.5882315766 region=water
H 7.7774908527 0.1513836830 0.4695977472 region=water
O 2.3326872723 1.2482041689 5.8422317338 region=water
H 3.2351249242 0.8859356300 5.5977797279 region=water
H 2.3859792023 1.3898413274 6.8201669750 region=water
O 4.6523554579 10.8009432497 5.7721953686 region=water
H 5.2867619957 10.8228424856 5.0662952558 region=water
H 5.1292896758 10.6085943826 6.5835421821 region=water
O 4.0389590298 7.1386005131 3.5977597940 region=water
H 4.9184290017 7.4344225303 3.7708177483 region=water
H 4.1720741651 6.5720641346 2.8813838876 region=water
O 8.1370379933 9.9999759556 7.2888013756 region=water
H 7.8771295877 9.0466426027 7.0397630389 region=water
H 8.7345031325 10.4127626381 6.6336367406 region=water
O 10.0656503243 10.4199569500 5.0869973451 region=water
H 10.6446317826 9.6539906607 4.8718236155 region=water
H 10.3930912061 0.2201131071 4.5684359281 region=water
O 2.5431151193 0.9684700723 8.4501159472 region=water
H 2.1618357467 0.1159180750 8.2617772273 region=water
H 3.3445843510 0.7779100516 8.9564082418 region=water
O 4.2604624764 10.8828558955 10.6184603770 region=water
H 4.1781301092 9.8333832238 10.5366180693 region=water
H 3.8013785963 0.1424933606 0.4621730042 region=water
O 9.0775276640 3.7103894239 2.5529470108 region=water
H 8.6940421680 4.0334078450 1.7778689108 region=water
H 9.9466097056 3.9220095026 2.3652616223 region=water
O 1.8807202054 9.2973254437 8.2431474946 region=water
H 2.0775219801 8.4653127770 7.7659523821 region=water
H 1.7951621259 9.1446189472 9.1828549000 region=water
O 10.4319183153 0.5267979579 10.1279761546 region=water
H 9.6375710850 0.9026166782 10.6497197526 region=water
H 10.1761276391 10.5196353848 9.8750818206 region=water
O 8.4912392399 7.5071687205 6.4496433666 region=water
H 9.2284527240 7.8560412425 5.9994018879 region=water
H 8.0473834460 7.0233739111 5.7184114987 region=water
O 9.7186275501 5.1416499563 7.7811311655 region=water
H 9.5152586133 5.6797209833 7.0218152321 region=water
H 9.9449753427 4.2785377121 7.4867974296 region=water
O 7.3706584181 9.2865406038 0.5138975475 region=water
H 6.5215556686 8.9380407533 0.1589565617 region=water
H 7.2160912926 9.0756790959 1.4759783012 region=water
O 5.8829839594 1.9541670924 9.7626679328 region=water
H 5.9302406738 1.7029708954 8.7810228974 region=water
H 4.9927928546 1.5971865119 10.0791764040 region=water
O 10.7628203583 7.8726173444 4.5313520510 region=water
H 10.9687416470 8.0338091844 3.6295485138 region=water
H 0.6551195239 7.9410195787 4.9983379116 region=water
O 7.5737014536 5.8314489999 4.3450665226 region=water
H 6.8539873473 5.3498459332 3.9476177328 region=water
H 8.2571606224 5.4468593458 3.7981392937 region=water
O 6.3155459715 10.9377883092 3.5996893713 region=water
H 5.8104191794 0.3887993636 2.8834992229 region=water
H 7.0550156207 0.5049852342 3.7776265067 region=water
O 0.4930190941 8.2247702798 1.8847114471 region=water
H 0.1274170817 9.1364694766 1.5562039237 region=water
H 1.2254450881 8.5112453812 2.5397394606 region=water
O 0.3450308302 1.4735420754 3.5601895859 region=water
H 1.1544398155 1.4577465799 4.0949123165 region=water
H 0.1060316403 2.4028204511 3.6702583421 region=water
O 2.7534426314 8.5788111581 0.5670875459 region=water
H 3.2910732214 8.1898179026 1.2542034655 region=water
H 2.2708580149 9.2158333089 1.0647033659 region=water
O 9.4983463013 8.9954407495 9.7510492440 region=water
H 8.8195316470 9.3392373230 9.0988056316 region=water
H 8.9394573574 8.9386357872 10.5863154397 region=water
O 7.7474894254 1.9166705642 7.7329175373 region=water
H 7.9515632866 0.9657989920 7.8670203468 region=water
H 8.5779382046 2.2247893995 7.4343130907 region=water
O 2.5960248118 6.7447772999 7.7631484655 region=water
H 2.2585020058 6.3588258099 8.5469495211 region=water
H 2.4481231680 6.0818953059 7.0610210289 region=water
O 2.2925573999 3.6669877963 9.5203756563 region=water
H 2.2534884572 2.8090415445 9.1607396709 region=water
H 3.1949787114 4.1546959599 9.3969314166 region=water
O 0.1664142529 6.7406296198 9.3586913333 region=water
H 10.8508652541 6.1884325024 8.5825444792 region=water
H 10.6876341749 7.6030269632 9.3581242937 region=water
O 2.7049149016 4.8295736737 5.6636129441 region=water
H 3.1763086096 4.1556449316 6.1399923377 region=water
H 3.3329399542 4.9270104566 4.9662543560 region=water
O 7.8421800686 4.6172584365 9.9135930563 region=water
H 7.3822511999 3.7785204888 9.7475030841 region=water
H 8.4525502292 4.8805664245 9.1816740116 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0 0 0 1
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0 1 0 0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0 -1 0 0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0 0 0 -1
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0 0 1 0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0 0 1 1
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0 0 -1 0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0 1 0 0
95 96 1.0
95 97 1.0
98 99 1.0 0 1 0
98 100 1.0 0 1 0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0 -1 0 0
122 124 1.0 -1 0 0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 15 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_015ps
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_010ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 30000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_010ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.1147542749 6.0176060194 8.2285985240 region=glycine
C 2.8468251535 6.6149948048 9.3962728167 region=glycine
C 2.8192966761 8.1331308340 9.4108380383 region=glycine
O 2.0819826563 8.7904362537 8.6893539203 region=glycine
O 3.5453126542 8.6371445187 10.4115344718 region=glycine
H 2.2747581712 5.0068139657 7.9769573805 region=glycine
H 2.2095342091 6.5937535898 7.3737371409 region=glycine
H 3.8889957255 6.1890710341 9.5079614506 region=glycine
H 2.2234242639 6.3306811015 10.4021488948 region=glycine
H 4.1246791113 7.8418034680 10.7550373248 region=glycine
O 5.6873558067 7.0265628109 3.0322670412 region=water
H 5.1745840684 7.8169790371 3.3135432734 region=water
H 5.7963493324 7.0163788906 2.0782578012 region=water
O 8.9306064130 3.1367712868 7.2331484785 region=water
H 9.0714318637 3.4550990885 8.1376849727 region=water
H 7.9817762092 3.0790338914 7.2257250241 region=water
O 0.3977825929 8.2433821682 4.0311172834 region=water
H 0.5497316147 9.2452205682 4.1493593353 region=water
H 10.6090325998 8.0905395510 3.5252968830 region=water
O 3.3486600222 4.7202829960 1.7375499065 region=water
H 2.5950402267 5.2894405255 1.6149519107 region=water
H 3.5462243736 4.5978768869 2.8052044007 region=water
O 0.1739304460 10.1020757518 0.5920333829 region=water
H 10.8974227614 9.2141821917 0.3426109216 region=water
H 1.0699852470 10.0351835207 0.9565348018 region=water
O 9.7931195255 4.6057565169 2.6700733286 region=water
H 8.9062295934 4.2245169500 2.6396628873 region=water
H 9.7023481933 5.4360712560 2.2199879034 region=water
O 6.2329049051 4.0061675392 6.2429772061 region=water
H 6.6568244716 4.6687923124 5.6753216821 region=water
H 6.1082351933 4.6447623172 7.0121888238 region=water
O 9.7358872787 7.4547113777 1.9059738671 region=water
H 9.7243798901 7.5968940206 0.9281641758 region=water
H 9.2477611828 8.2072245717 2.2161494967 region=water
O 4.7269501141 1.3902019985 5.6993350990 region=water
H 4.8631190900 1.0512898405 6.5937818185 region=water
H 5.0531527874 2.3314882327 5.7774788585 region=water
O 5.4394563836 6.4133416669 0.4733185914 region=water
H 6.2528403375 6.3194531812 10.8972146266 region=water
H 4.9837668656 5.5711452904 0.3029854703 region=water
O 2.8010881312 0.1602373421 1.7677233517 region=water
H 2.0245508903 0.5155762354 2.1123049665 region=water
H 3.0920481153 10.4829771400 2.3324410376 region=water
O 9.3777839951 1.7820230635 3.5398885260 region=water
H 9.5082975230 2.6036508483 3.1773123194 region=water
H 8.4229974593 1.5490921345 3.5331278367 region=water
O 5.4218073647 1.0430197594 0.5629384968 region=water
H 4.8573705716 1.6619061982 0.0703277858 region=water
H 4.9302308075 0.5015535964 1.1538088071 region=water
O 4.3158133309 3.2554977198 10.5195368693 region=water
H 3.9796084221 3.6916757899 0.4178254307 region=water
H 3.4564920552 3.1997084735 9.9816916742 region=water
O 0.7065144310 10.9046241856 3.9772825518 region=water
H 0.0155435833 0.2991483254 3.4390322358 region=water
H 0.8316401986 0.5029880099 4.7544617765 region=water
O 10.4415243215 7.8750429721 10.0883267155 region=water
H 10.9440196072 8.2290875481 9.4028448070 region=water
H 9.7015771788 7.6241033482 9.6139660912 region=water
O 5.1216486446 8.0753370366 6.8068572065 region=water
H 4.1643126739 8.1937755482 6.5354826357 region=water
H 5.2448570444 8.7598958958 7.4835701362 region=water
O 9.2884574520 3.7247525545 10.2591788472 region=water
H 8.7429080493 3.6346978699 0.0946376543 region=water
H 9.7002463400 2.8115112421 10.1924660670 region=water
O 1.9176390438 0.5422285625 8.5251859676 region=water
H 1.1456609327 0.8396697168 9.0674987998 region=water
H 1.8779713221 10.5471595262 8.5379618737 region=water
O 10.5657739174 0.9935335288 9.7907971390 region=water
H 10.1768320970 0.6176973052 8.9306742339 region=water
H 10.6701589567 0.2170809678 10.4663620180 region=water
O 9.1794359894 8.4306017312 5.7795353651 region=water
H 9.9714571413 8.3767607903 5.2349327025 region=water
H 8.6893524506 7.6232270217 5.7333434514 region=water
O 4.7845105477 10.8194440755 8.1353846329 region=water
H 5.3104607256 0.5982967756 8.5350062857 region=water
H 3.8451198822 0.0218526435 8.4125877351 region=water
O 1.4633469067 3.2959430701 9.9403013666 region=water
H 1.5140701497 3.5798215191 9.0008615301 region=water
H 1.1309872357 2.4429969502 9.8263069927 region=water
O 5.5270691688 5.7765029409 8.4377515445 region=water
H 6.5294046349 5.7778984287 8.8207985688 region=water
H 5.4044354227 6.5816071572 7.8690119071 region=water
O 10.6450086679 4.2467607235 5.3535284613 region=water
H 10.4471529633 4.1966281030 4.3818935834 region=water
H 9.8175625322 4.0023064464 5.8170086639 region=water
O 6.5713512389 9.0985272555 10.8192236392 region=water
H 5.9225104115 8.4057449625 10.9723713839 region=water
H 6.0273937031 9.8823929167 10.8674730977 region=water
O 7.9818765558 9.8283255990 2.3708759163 region=water
H 7.4694738181 9.6917214219 1.6080611654 region=water
H 7.6303919258 10.5259405024 2.8878521387 region=water
O 1.1951471787 6.2753158505 0.9841870271 region=water
H 0.3819942297 5.9218269262 1.4183572150 region=water
H 0.7093358266 6.7137475371 0.2346981108 region=water
O 7.1634906431 6.3234238359 5.6011000607 region=water
H 6.8557072140 6.6984495362 4.7367714390 region=water
H 6.4092809086 6.7206269314 6.0784750868 region=water
O 9.9028472010 6.3727699684 7.4246008169 region=water
H 9.8807054415 5.7391066958 6.6277599440 region=water
H 9.9432767728 7.3420013519 7.0658525644 region=water
O 5.9197909796 2.2389985051 8.4812212175 region=water
H 5.6924942134 2.9589196475 7.7638580507 region=water
H 5.6846790702 2.6858835771 9.3462696399 region=water
O 3.9273215765 4.6673753847 4.6526498388 region=water
H 3.5615264782 5.3906977517 5.1296703419 region=water
H 4.7598392914 4.3527110194 5.1433730905 region=water
O 4.1368196247 9.2059406544 3.9379341738 region=water
H 4.6371444123 9.0334016740 4.7215735363 region=water
H 3.1932695957 9.0673905351 4.0763610702 region=water
O 9.3367553405 10.7443239053 7.5282238982 region=water
H 8.5718472852 0.3191065770 7.6216254873 region=water
H 9.1114137477 10.2564780305 6.7717934096 region=water
O 6.5443282708 1.0221868886 3.5938691448 region=water
H 5.9185975072 0.9553200813 4.3126760396 region=water
H 6.0477986658 1.1723400999 2.7897212294 region=water
O 1.7618550002 3.6040194676 7.0042076859 region=water
H 0.9647179636 3.9420208189 6.5884419062 region=water
H 2.0533963886 2.7007332873 6.6051071107 region=water
O 2.3129766434 6.7995174399 5.5305363335 region=water
H 1.6555173533 6.0547610625 5.4041950734 region=water
H 1.7842712108 7.5725546172 5.2526284994 region=water
O 7.9403466948 6.2530282440 9.5030912901 region=water
H 8.3512141860 5.4840727220 9.8526172867 region=water
H 8.3848023249 6.4444126878 8.6422928670 region=water
O 1.9797983523 1.1803783342 5.9242764219 region=water
H 3.0283925332 1.1876898133 5.7774385824 region=water
H 1.9137644630 0.8679226760 6.9274337850 region=water
O 7.1468186287 3.7110607279 1.2312915314 region=water
H 6.8385511526 2.8606630729 0.6994164224 region=water
H 6.2761200067 3.9974216397 1.5237493470 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0 -1 0 0
20 21 1.0
20 22 1.0
23 24 1.0 -1 0 0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0 0 0 -1
38 40 1.0
41 42 1.0
41 43 1.0 0 -1 0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0 0 0 1
50 52 1.0
53 54 1.0 0 1 0
53 55 1.0 0 1 0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0 0 0 1
62 64 1.0
65 66 1.0
65 67 1.0 0 -1 0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0 0 1 0
74 76 1.0 0 1 0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0 0 1 0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 20 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_020ps
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_015ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 40000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_015ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.4027999254 7.1346402935 6.8166805966 region=glycine
C 3.2991967373 8.2822598660 6.4614094648 region=glycine
C 3.8303228964 9.0750725491 7.6608447173 region=glycine
O 4.2044641671 10.1914881994 7.5031679613 region=glycine
O 3.9563542669 8.4478875562 8.8461761116 region=glycine
H 2.8563595757 6.2169804735 7.1185242561 region=glycine
H 1.5005790327 7.3612999433 7.2590503779 region=glycine
H 2.8678729832 9.0666469918 5.7243693883 region=glycine
H 4.1611543900 7.7776490535 6.0207818100 region=glycine
H 3.3969362988 7.6409812514 8.7559751842 region=glycine
O 8.6830661219 6.2158917227 2.2508661795 region=water
H 9.5796596503 6.0950359094 2.0919139872 region=water
H 8.2658218623 6.8435367648 1.5688397858 region=water
O 10.7098814503 3.9592951791 7.0513995992 region=water
H 10.4046011156 4.1090420306 6.1214362125 region=water
H 10.1715750254 4.6545712869 7.5044123921 region=water
O 10.5037940320 6.4143642753 4.9218236023 region=water
H 10.9076975365 6.2607888475 4.0495719590 region=water
H 10.3225449009 7.3576528651 4.8459833684 region=water
O 4.9322668305 6.4097185683 0.5001727650 region=water
H 4.2601367636 6.1975092254 10.7950535548 region=water
H 4.4016542264 7.1075014440 1.0039676778 region=water
O 1.4060463354 0.8253965994 7.8360489525 region=water
H 1.7871897150 1.5036161488 8.3573478871 region=water
H 2.1722345393 0.2994606294 7.7835056190 region=water
O 6.1966786406 4.9336782301 2.7102436769 region=water
H 5.8445238851 5.5014539285 1.9954785333 region=water
H 7.2049561914 4.8985299026 2.4826729906 region=water
O 5.9099939199 3.3119010646 6.7035862162 region=water
H 6.4474814770 2.8024902824 7.4100349631 region=water
H 5.6488051810 4.1440683874 7.1997032958 region=water
O 9.1626100282 3.6509882322 4.4395674922 region=water
H 9.3326486149 4.5255025323 4.1155010907 region=water
H 8.2194033570 3.3473919058 4.4813204851 region=water
O 2.5720012756 2.7480316536 10.4229628815 region=water
H 3.4696971300 2.5112401182 10.4474151717 region=water
H 2.5334842677 3.7521062299 10.4529979450 region=water
O 0.7808154991 5.7886588168 2.4190174841 region=water
H 1.5418975132 5.5970474597 2.9633735143 region=water
H 0.2649331346 4.9382986570 2.3074530925 region=water
O 3.1292098263 9.8468621317 3.5876853133 region=water
H 3.5786301248 10.7365347755 3.8154900198 region=water
H 3.2563141606 9.7252397853 2.6369804442 region=water
O 4.9782776928 0.8343906317 4.8940796010 region=water
H 5.1821306990 0.1402536146 5.5350262130 region=water
H 5.1877786110 1.5875242420 5.4403529695 region=water
O 3.2891430159 8.8937086155 0.9285423206 region=water
H 2.4681968615 9.3559068442 0.6575480813 region=water
H 3.6279000841 8.5343751231 0.0706584210 region=water
O 4.4000308964 0.3750670074 1.4787140676 region=water
H 3.8810606344 10.6246957995 1.0087496445 region=water
H 4.9612841282 0.7007013894 0.7881987040 region=water
O 1.0212370765 0.2392135129 2.0988215265 region=water
H 0.9743582512 1.1008423749 2.4980199113 region=water
H 1.4954647375 10.5872611284 2.6615183995 region=water
O 10.2410289397 8.6381417803 1.7725152038 region=water
H 10.7046708368 9.0837847197 2.5204463585 region=water
H 9.4461970349 8.3793357827 2.0513562477 region=water
O 8.8547254960 9.3868869475 8.0607242679 region=water
H 8.8836362963 10.0278546088 7.3410569614 region=water
H 8.4539802745 8.6075650704 7.6370716315 region=water
O 10.1027170864 3.1860415759 10.5733804000 region=water
H 10.2257942232 3.8297111040 9.9015769430 region=water
H 10.1902080017 2.2693770770 10.1226767377 region=water
O 5.2337460446 0.1860753803 9.8066883677 region=water
H 6.1502007331 0.4608413991 9.6206501503 region=water
H 4.8714482526 10.6728862890 8.9969261480 region=water
O 10.9574813205 0.3759534989 10.0593130522 region=water
H 0.6603213599 0.4823388149 10.7808040657 region=water
H 0.5547011958 0.2966152968 9.2347836317 region=water
O 7.9584685942 10.5949551877 5.5500509382 region=water
H 7.8465545660 0.2123410377 4.8559816560 region=water
H 7.7471881504 9.7563922080 5.0841850776 region=water
O 7.4726469739 1.9706038294 8.4804944348 region=water
H 7.7766362151 1.0656478407 8.6848201062 region=water
H 7.3486780613 2.4590817378 9.3435249838 region=water
O 2.8874368558 5.7420411349 9.5332730815 region=water
H 2.1101128663 6.1746997034 9.9565808935 region=water
H 2.5346459185 5.2502278171 8.7087261127 region=water
O 7.1978008312 6.8025776176 7.1664780919 region=water
H 6.4686976875 6.5961897100 7.7388543922 region=water
H 6.7954790995 6.6081091012 6.2645009596 region=water
O 2.2072152323 2.4669281386 3.7824479899 region=water
H 1.8403619060 2.9946834570 3.0147918049 region=water
H 2.6901387081 3.1093752430 4.3450920156 region=water
O 8.0596620020 0.0720584573 10.0556233509 region=water
H 8.9638214933 0.3032470960 10.3169192392 region=water
H 8.2082346350 10.1334622429 9.6114119171 region=water
O 7.4448472300 7.4425009166 0.1740824895 region=water
H 6.5643846813 7.0434070998 0.1066959002 region=water
H 7.9196570729 7.1152203292 10.3758724933 region=water
O 0.0508049500 3.0900547305 2.1887393053 region=water
H 10.4236093770 2.8937822987 2.8429889054 region=water
H 10.5205438533 2.9087827555 1.2878696754 region=water
O 5.7931051758 6.6972668191 4.6056936580 region=water
H 5.7485354905 6.1605013992 3.7630737613 region=water
H 6.1323941290 7.5470747188 4.2746595115 region=water
O 0.6325099005 7.1900090982 0.0434059502 region=water
H 0.9978597877 6.6555793519 0.7208958829 region=water
H 0.3138054400 7.9909596587 0.5488732028 region=water
O 7.0505824114 3.8388987963 0.3168969729 region=water
H 6.5175770579 3.9133797503 1.0988532548 region=water
H 7.9159039479 3.6489192675 0.5006298130 region=water
O 5.7953328512 4.8838936651 8.9319164816 region=water
H 6.3502813815 4.4753878488 9.6982909690 region=water
H 4.9661326406 5.1177643237 9.3744733754 region=water
O 2.8194862026 5.2828216432 4.4286400864 region=water
H 2.4457811147 6.1080707932 4.7590558272 region=water
H 3.6729160052 5.5565475675 4.0641939548 region=water
O 10.5263430107 9.4950637722 4.8378272755 region=water
H 0.0248726278 10.3074084534 4.8039581078 region=water
H 9.6129121798 9.8345447310 5.1353132772 region=water
O 7.2899193491 0.0481973782 1.9734805140 region=water
H 6.3580151828 0.0574410054 2.1126975731 region=water
H 7.2625487216 10.7542923674 1.0615473931 region=water
O 2.3420746635 4.4807483801 6.9317105088 region=water
H 2.4698634168 4.7032591624 5.9204548324 region=water
H 1.3983374729 4.3670481762 7.1311948327 region=water
O 0.0065051085 7.6522242322 8.3508069356 region=water
H 10.2258284942 8.3708392051 8.2298053521 region=water
H 0.0478521940 7.5243816613 9.3286017922 region=water
O 9.0965591625 5.5285835353 8.6541663091 region=water
H 9.6933472151 6.3348879325 8.5960525458 region=water
H 8.2984598249 5.7604998867 8.0656536443 region=water
O 0.4430497246 1.1355936986 5.2501586593 region=water
H 0.6365592624 1.0326511564 6.2137263091 region=water
H 1.1187580774 1.7891028757 4.9287150027 region=water
O 7.3463205717 8.6097982935 3.5288688137 region=water
H 7.1550114418 9.3781599026 2.9612695159 region=water
H 7.4954451449 7.8578163314 2.9453605626 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0 0 0 -1
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0 0 -1 0
50 52 1.0
53 54 1.0
53 55 1.0 0 -1 0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0 0 -1 0
68 69 1.0 1 0 0
68 70 1.0 1 0 0
71 72 1.0 0 1 0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0 0 -1 0
89 90 1.0
89 91 1.0 0 0 -1
92 93 1.0 -1 0 0
92 94 1.0 -1 0 0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0 1 0 0
110 112 1.0
113 114 1.0
113 115 1.0 0 -1 0
116 117 1.0
116 118 1.0
119 120 1.0 -1 0 0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 25 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_025ps
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_020ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 50000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_020ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 3.6389385596 8.6052134140 4.1040963333 region=glycine
C 4.5037687850 9.3997282547 5.0692049360 region=glycine
C 3.7526530451 10.2616650806 6.0692546582 region=glycine
O 4.2288249227 0.3247019784 6.4098835033 region=glycine
O 2.5699821526 9.8550701927 6.6078907391 region=glycine
H 3.8085016847 7.6401908714 3.9034613596 region=glycine
H 2.6103473395 8.6104637946 4.1758948770 region=glycine
H 5.1989076734 10.0261465879 4.4371512377 region=glycine
H 5.1137632930 8.5234576541 5.4389749356 region=glycine
H 2.4601017777 8.9811707773 6.0608296961 region=glycine
O 10.1527621817 4.0004983810 10.3107514000 region=water
H 10.6237901117 4.8146035826 10.1314893054 region=water
H 10.8110217675 3.2429249820 10.1884894277 region=water
O 6.8794845222 2.3131879150 8.7266494136 region=water
H 6.7404797744 1.3878701966 8.9961713435 region=water
H 7.1139451582 2.8544282054 9.5211747595 region=water
O 1.4812203052 2.2726959046 9.8610368071 region=water
H 2.2441650488 2.4975392890 10.4150337371 region=water
H 1.8262931364 1.4050794357 9.4864009936 region=water
O 4.5876614490 5.8553606026 3.8968307364 region=water
H 4.1727319110 4.9966794838 4.3008740994 region=water
H 4.9213154098 5.6796198092 2.9827723486 region=water
O 10.1913851346 3.5753393074 5.5602940701 region=water
H 9.8216998912 2.7194111297 5.3922395926 region=water
H 0.0523966140 3.4680705469 5.9678531688 region=water
O 7.2725206279 4.8587089755 7.1237327394 region=water
H 6.5532885506 4.2922300721 7.1198779919 region=water
H 7.3825595075 5.1360172150 6.1514655092 region=water
O 4.4590868686 2.6582923025 7.5923849302 region=water
H 5.3686331455 2.5260877247 8.0093624127 region=water
H 4.1927436393 1.7525124207 7.2580213438 region=water
O 9.2361397540 0.6839845024 5.1460773770 region=water
H 9.2224214523 10.8475711013 4.5522519098 region=water
H 8.3312238684 0.9675790429 5.1024808473 region=water
O 7.3092818059 4.6236010199 10.2700050413 region=water
H 8.2978650567 4.4931940105 10.2380814159 region=water
H 7.1155413495 4.5931912044 9.2696612823 region=water
O 7.6125375469 3.6347948291 2.5460944810 region=water
H 7.8921258896 4.3857944483 3.0642745247 region=water
H 8.2767446363 3.4565142628 1.8614107015 region=water
O 4.3130950034 0.8596270662 1.1581724542 region=water
H 4.0482560497 1.7506263648 1.2775337830 region=water
H 4.3471581503 0.6788775954 0.2511874839 region=water
O 3.7682534382 3.6424353823 5.1973491278 region=water
H 3.6262065327 3.5480427570 6.1382445667 region=water
H 2.9712414562 3.2230550417 4.8008539624 region=water
O 0.4574651234 10.6851156841 8.5841594892 region=water
H 0.7987793151 10.4676507596 9.4628453092 region=water
H 0.9276518461 10.0471157299 8.0025622969 region=water
O 6.9280630859 10.7854233827 9.8482697537 region=water
H 6.7580836036 9.8666713278 10.2627667203 region=water
H 7.7282612217 10.5496567299 9.3790527411 region=water
O 6.3446620665 2.0485381110 4.8947579942 region=water
H 6.8601276564 2.5829409997 4.2784485961 region=water
H 5.4309431922 2.4189699419 5.0511561629 region=water
O 0.9579206901 10.4383173537 3.3633168141 region=water
H 0.1887361387 9.9416126491 3.4934224178 region=water
H 1.6415023561 9.8540620614 3.5854037064 region=water
O 10.4929912073 6.0562505374 6.7153209886 region=water
H 10.8686172100 5.7670195490 7.6008383808 region=water
H 10.1685690449 5.1484282065 6.4650077785 region=water
O 5.4506228705 6.4917886364 8.2277272747 region=water
H 6.0162540506 6.3126208159 8.9938063851 region=water
H 5.8756353781 6.0829819221 7.4159871248 region=water
O 5.3990049862 4.9011416021 1.5773749251 region=water
H 5.5249569655 5.1656765856 0.6469754454 region=water
H 6.2837671368 4.4367763171 1.8511376594 region=water
O 1.8153170121 2.1187110987 3.9407456203 region=water
H 2.3836060696 2.5830187052 3.2692055165 region=water
H 1.7570322141 1.1337862038 3.7969970051 region=water
O 7.1387342507 8.5275985641 6.2958451356 region=water
H 6.6626139351 7.9332433958 6.9169815774 region=water
H 7.8678533928 8.9074220916 6.9276680906 region=water
O 0.2202997224 1.5097554687 1.2344129878 region=water
H 0.6495038076 1.4011524712 2.0876807801 region=water
H 0.8590491273 1.3762398433 0.5445058679 region=water
O 6.2588761143 10.8968445483 3.0156533408 region=water
H 6.4773630529 0.7303271530 3.5852840069 region=water
H 5.5144245984 0.2979740209 2.4418664700 region=water
O 3.2448504647 6.6193390843 9.6141906090 region=water
H 3.2879485274 6.6965511063 10.5431577871 region=water
H 4.1448549758 6.7051812919 9.2617942382 region=water
O 9.3344883046 9.3653717720 3.4759454531 region=water
H 8.7041501761 9.5915758875 2.7696794235 region=water
H 9.2647503651 8.4356888277 3.5340579697 region=water
O 3.9064147452 0.1139756792 9.4333221179 region=water
H 4.8289994047 0.2522913555 9.2080491180 region=water
H 3.5730378376 10.7798700728 8.5975267564 region=water
O 6.1762833360 8.2828610880 2.1728551074 region=water
H 6.5996346921 9.0819429701 2.6046940114 region=water
H 5.6150870821 7.9834160678 2.9119523050 region=water
O 1.4125280877 9.5807654767 0.2347376655 region=water
H 2.0157725064 8.9594615622 0.5270713627 region=water
H 1.3105519462 10.0179283719 1.0303179533 region=water
O 9.8101118451 7.7240983470 0.6095473550 region=water
H 9.8557207372 7.3611536932 1.5268052435 region=water
H 9.6173077914 8.6524118640 0.7365871677 region=water
O 2.7149542259 3.1195423392 1.4984653870 region=water
H 2.4653344397 4.0406502410 1.8418648230 region=water
H 1.8646694108 2.6423771925 1.3439400270 region=water
O 6.4883781732 7.6071111556 10.4051106589 region=water
H 7.1428328266 6.8828196453 10.5125087623 region=water
H 6.5899558985 8.0432335567 0.3200900536 region=water
O 2.9088404852 6.6616612132 1.4235128078 region=water
H 3.6272693049 6.1270548813 1.6709096295 region=water
H 2.1036393778 6.2386184435 1.7607464345 region=water
O 0.7721218060 4.7817035483 1.8527008208 region=water
H 0.1599420927 4.3483527159 1.2850593140 region=water
H 0.2016466812 5.1126977674 2.6145170165 region=water
O 9.8326355190 6.2362316749 3.2902255500 region=water
H 10.3848053817 6.5594949410 4.1105965659 region=water
H 9.0471201269 5.8750115821 3.6164743690 region=water
O 8.8775224549 10.5502668403 0.8716569514 region=water
H 8.1673479048 0.0628612555 0.5409347860 region=water
H 9.4004793222 0.2327332212 1.3012482195 region=water
O 1.4706138137 3.6063475803 7.3550848284 region=water
H 1.2720855511 3.5445234786 8.3064447024 region=water
H 2.3986743865 3.3935931478 7.3831342872 region=water
O 1.0242584864 8.1149460973 5.3341737404 region=water
H 0.4059007218 8.6400963131 4.7835762648 region=water
H 0.4902198110 7.5353187482 5.9755036545 region=water
O 7.2787450963 6.3403580835 4.5502852298 region=water
H 6.3788650598 6.2961279467 4.1053425800 region=water
H 7.1836238042 7.1636270554 5.1016945813 region=water
O 8.9514713595 10.2315725627 7.4744300747 region=water
H 9.9236875511 10.2716586392 7.7276135634 region=water
H 8.9745122404 10.6695233671 6.5565147639 region=water
O 0.4681877467 6.2636172371 9.6472753810 region=water
H 10.9157686209 6.8626156008 10.2587283399 region=water
H 1.3642472098 6.6225540081 9.6384018658 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0 0 1 0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0 1 0 0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0 0 -1 0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0 0 1 0
77 79 1.0 0 1 0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0 0 -1 0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0 0 0 1
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0 0 1 0
113 115 1.0 0 1 0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0 -1 0 0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 30 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_030ps
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_025ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 60000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_025ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.5721479767 7.7038281768 6.0815662823 region=glycine
C 3.3148805582 9.0413399756 6.0877631348 region=glycine
C 2.8914636626 10.0890581464 5.0400782566 region=glycine
O 3.4982890333 0.0922679671 4.7992345994 region=glycine
O 1.5940621681 9.8693856405 4.5278967813 region=glycine
H 3.2165171317 6.9319959853 5.9921193889 region=glycine
H 2.1754836138 7.6101262141 7.0362530811 region=glycine
H 4.4610631969 8.8417797823 5.8780684966 region=glycine
H 3.2837241073 9.4453821611 7.1471121761 region=glycine
H 1.5755613066 8.8418847212 4.5793019921 region=glycine
O 2.2504346219 3.3001651848 0.9328335037 region=water
H 1.4321888216 2.8469701115 1.0657049067 region=water
H 2.1798008571 4.2890713862 0.8225739580 region=water
O 0.4390173875 1.9193989130 6.7039098581 region=water
H 1.2880986432 1.4035853794 6.4390999367 region=water
H 10.9504924667 1.9168909519 5.8371310205 region=water
O 1.5934256210 10.6295066222 1.6731487832 region=water
H 1.4785272162 9.7696163208 1.2285356852 region=water
H 1.5125856301 10.5704382319 2.6569307764 region=water
O 1.3293271837 6.7975145594 3.5669483326 region=water
H 0.9562700299 6.3935634711 4.3431076660 region=water
H 2.1568597302 6.3044883375 3.3592097781 region=water
O 10.5473535240 7.7777937144 5.9584221684 region=water
H 10.1163881423 6.8771812494 6.1181265386 region=water
H 0.4041135497 7.5240149322 5.6450996664 region=water
O 5.6104021548 3.2747063957 5.8334163930 region=water
H 5.7695278145 2.3980476807 6.2755996650 region=water
H 6.3314345876 3.4460128493 5.1519075913 region=water
O 10.6656711475 1.0545146540 9.5120261050 region=water
H 10.9417168831 1.0710568759 8.5758704021 region=water
H 0.5021679413 1.2266879645 9.9857345645 region=water
O 8.5282440423 2.9605455661 5.0007411242 region=water
H 8.2059028229 3.6515877292 4.3270507501 region=water
H 8.3844830726 2.0836070183 4.6326202670 region=water
O 6.6279743133 4.7685142617 3.9789966346 region=water
H 7.3119624627 4.8769866226 3.2439596886 region=water
H 5.9282763618 5.4000475414 3.8654077850 region=water
O 8.3728546106 2.5878355476 9.1770348006 region=water
H 9.2341874947 2.3341023993 9.3428394052 region=water
H 8.0289667097 1.8715950605 8.6860278014 region=water
O 5.9958973123 8.2069957157 5.2390033188 region=water
H 5.8047162729 7.3644494748 5.6219261216 region=water
H 5.4026025768 8.1985557707 4.4652943256 region=water
O 8.1677834767 5.8616459196 2.1635538080 region=water
H 7.9370304580 5.5125953450 1.2549271096 region=water
H 7.7824986092 6.7002697315 2.0660276955 region=water
O 10.5005389015 1.8902061316 1.8489923695 region=water
H 9.9821106954 1.6614217354 2.6401147094 region=water
H 0.0957805526 1.0870082402 1.8465697207 region=water
O 8.5984232249 9.0373320896 1.7260598119 region=water
H 8.7571582139 9.8341306754 1.1350856375 region=water
H 9.4167704928 8.5478429706 1.6437668719 region=water
O 6.7137284933 4.2450787937 0.1434511343 region=water
H 7.4111018682 3.7214086418 10.6182501724 region=water
H 6.0621873450 3.5663610925 0.4311626497 region=water
O 4.6716748349 5.8713989034 6.5012396940 region=water
H 4.9667100562 5.0997149564 5.9744730950 region=water
H 4.7357430203 5.5750734007 7.4012607862 region=water
O 8.9241189352 8.1231086855 8.7802349545 region=water
H 8.9468248965 8.3492549792 7.9278112443 region=water
H 9.7627070443 8.3146424597 9.2056942623 region=water
O 2.5874642576 0.9655962708 8.0975057888 region=water
H 3.3232564244 1.5128892420 8.3962507778 region=water
H 2.7823547601 0.0062826554 8.3948703459 region=water
O 5.2213549266 1.7326950308 8.4552876579 region=water
H 5.5806611033 0.8050964710 8.4462550493 region=water
H 5.3016593955 1.9109240337 9.4045190048 region=water
O 3.7517938544 5.4624205031 2.8130475886 region=water
H 3.3433987233 5.6746927133 1.9461554473 region=water
H 3.5730773736 4.5258407543 2.9161324967 region=water
O 10.6510261026 5.0059761482 4.8338289221 region=water
H 10.4848891852 4.8160486891 5.7259473336 region=water
H 10.0916505471 4.3627511095 4.3947432112 region=water
O 6.6335316664 0.9334743907 1.5928111208 region=water
H 6.8761875328 0.4536020175 0.7448332779 region=water
H 7.0834702810 0.4004062226 2.2254410311 region=water
O 5.8936115567 7.2817306415 9.4309628764 region=water
H 5.9066181849 6.3222127680 9.6069231228 region=water
H 6.8462323384 7.4962715965 9.4475689485 region=water
O 2.4785868416 5.9167029970 0.2580639835 region=water
H 2.5140024214 5.8719926576 10.2694355035 region=water
H 1.9127879661 6.6852809675 0.3922583840 region=water
O 8.5001576079 9.5221446668 5.5033549137 region=water
H 9.2012908684 8.8045380049 5.6042096302 region=water
H 7.6707251308 9.0079403997 5.3327987149 region=water
O 3.2169446926 9.2812607366 9.2300235521 region=water
H 3.8280911673 8.6691626338 9.4450614070 region=water
H 2.3551183532 8.9168947814 9.4533960782 region=water
O 8.9476376230 4.9333762497 7.3971182069 region=water
H 8.7893087741 4.2967444657 6.6960715069 region=water
H 8.6458408363 4.3648070605 8.1044210626 region=water
O 0.2566232144 9.2691823258 9.6106097399 region=water
H 0.2120587084 8.9807120549 10.5275630963 region=water
H 10.8426180203 10.2209390995 9.6377804090 region=water
O 9.4688604825 0.5545994834 3.9722481288 region=water
H 9.3523082965 10.7025232165 4.4621513633 region=water
H 10.1024485754 1.0504501684 4.5331850054 region=water
O 4.6578189047 2.3090966795 0.2228889782 region=water
H 4.0949083780 2.7994241095 0.8157775311 region=water
H 5.0607324645 1.6524201050 0.9307901331 region=water
O 6.1259316182 7.7560335160 1.1849120238 region=water
H 6.1190215208 7.5153006497 0.2466044868 region=water
H 6.8818863834 8.3531535846 1.2972603198 region=water
O 4.4425261471 8.2531899345 3.1571094301 region=water
H 5.0994445329 8.3559379432 2.3835884457 region=water
H 4.1068657204 7.3292189964 3.0866319659 region=water
O 2.7579718235 3.0065764808 4.0689698099 region=water
H 3.5124664942 3.2785364586 4.5630490829 region=water
H 2.9958139910 2.0529644020 3.9881261359 region=water
O 0.3470874762 7.9979047715 1.3479909333 region=water
H 0.2218193516 7.1634932253 0.8481622947 region=water
H 0.4485075024 7.7808910792 2.2796284913 region=water
O 8.0621850297 10.7571691865 10.5809337855 region=water
H 7.6377821489 10.6622248188 9.7284388530 region=water
H 8.7507854355 0.4023032486 10.3126249799 region=water
O 10.5523588607 4.6291729768 0.9576364955 region=water
H 10.4802867949 3.7148344790 1.0981903666 region=water
H 0.3015821368 4.8231447749 1.5529306627 region=water
O 1.7530165929 6.8464431593 8.6534649356 region=water
H 1.4278649005 5.9661064726 8.4897899650 region=water
H 1.0338215458 7.4874465478 8.6755998893 region=water
O 5.5004279319 4.5331614489 8.7747783841 region=water
H 5.0389922119 3.7097500403 8.4073691118 region=water
H 5.8873273009 4.2163715198 9.6486327113 region=water
O 6.4339381954 9.9859359553 8.2922851195 region=water
H 6.1334810888 9.8840725706 7.3927337703 region=water
H 6.6868176978 9.0905422562 8.4641241334 region=water
O 0.6401426069 4.5356146107 7.9711577105 region=water
H 10.5743460185 4.7725570823 7.9784487586 region=water
H 0.7557895187 3.6627576400 7.5908818629 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0 0 1 0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0 -1 0 0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0 1 0 0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0 1 0 0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0 1 0 0
50 51 1.0
50 52 1.0
53 54 1.0 0 0 -1
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0 0 0 -1
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0 -1 0 0
95 96 1.0 0 -1 0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0 0 1 0
116 117 1.0
116 118 1.0 1 0 0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0 -1 0 0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 35 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_035ps
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_030ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 70000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_030ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.4670141261 9.4685379494 4.2569521686 region=glycine
C 3.1882950928 10.5129915104 4.9988016058 region=glycine
C 2.3802823042 0.6801582973 5.5705676636 region=glycine
O 2.9055069600 1.7706704616 5.6539695085 region=glycine
O 1.2207559584 0.4089266626 6.2157959000 region=glycine
H 2.9066506065 8.4946896730 4.0563097506 region=glycine
H 1.5127590033 9.3534327815 4.5747167991 region=glycine
H 4.1148458829 10.8150011310 4.4653150179 region=glycine
H 3.5734574710 10.1204917594 6.0225805723 region=glycine
H 1.1511233231 10.4001560727 6.0091294514 region=glycine
O 6.1328527388 1.6811523683 0.3947443637 region=water
H 5.4943548494 2.3483780629 0.6044511333 region=water
H 5.6559790440 0.8612558550 0.3835911705 region=water
O 1.1283738066 5.4647905065 10.2487040123 region=water
H 1.7325994202 4.9624747817 9.7508375173 region=water
H 0.3428998520 5.1088112731 9.8592546136 region=water
O 0.9448949996 2.0768330562 1.5476422792 region=water
H 0.1959858168 2.4121076623 2.1217899068 region=water
H 0.5678441948 1.4635926003 0.9440091985 region=water
O 0.6875904976 10.0194337479 2.0639721399 region=water
H 0.8861155776 9.7254803348 1.2175058988 region=water
H 1.6136758824 9.9440460324 2.4843436284 region=water
O 6.8506866107 9.1150760306 2.8407767675 region=water
H 6.8838182280 9.9688202846 3.3126581374 region=water
H 6.1414612928 9.2986154378 2.2168382798 region=water
O 5.2804362754 1.2288115003 8.5372797893 region=water
H 5.6854536793 1.1331403341 9.4057626426 region=water
H 5.7555199208 2.1031786996 8.3312763088 region=water
O 8.8532965357 0.4821726167 4.4651567252 region=water
H 9.4694212628 1.3174375609 4.3890685224 region=water
H 8.9466972656 0.1238488760 5.3696826008 region=water
O 10.5650424798 3.8024938889 5.9386210679 region=water
H 0.3349207260 3.7353842116 6.5112114041 region=water
H 10.2736861781 4.7340951625 5.7906827792 region=water
O 7.1273278520 3.4988922044 7.6591568529 region=water
H 7.1149736457 4.0066499629 6.8933953143 region=water
H 7.5215609347 2.6459936476 7.4405878834 region=water
O 9.5116508850 1.0800442690 10.1596749098 region=water
H 10.2655333416 0.5043157008 9.8631291910 region=water
H 9.3263689147 0.8431713913 0.1221625923 region=water
O 6.0071373790 0.2971669502 4.6789299496 region=water
H 6.9233413661 0.2986424530 4.7982729731 region=water
H 5.5964646598 10.9091926379 5.5326460545 region=water
O 7.5744886858 5.7178179385 9.2934162837 region=water
H 8.5361495032 5.5904958406 9.1834021360 region=water
H 7.1527175090 4.8821992419 9.0839809135 region=water
O 2.1101485245 4.7065318595 3.8397286376 region=water
H 2.9385351400 4.4399954921 3.3412150684 region=water
H 1.4710372594 4.8638387258 3.1766348394 region=water
O 3.2654431152 7.7215628688 0.6863982425 region=water
H 3.6943143490 8.5568749458 0.7916954165 region=water
H 3.9628335147 7.1479227163 0.2061109746 region=water
O 5.0181171725 3.0013951721 4.0479436747 region=water
H 4.2169346141 3.1337329781 4.6036396042 region=water
H 5.0256743296 2.0734063203 3.9400913408 region=water
O 3.7868937596 6.9653341863 4.5967302367 region=water
H 3.4912601800 7.4187426164 5.4712907792 region=water
H 3.0765687941 6.3025257653 4.3502217944 region=water
O 7.0326067936 7.3593926980 4.9189926030 region=water
H 6.1090370491 7.2841262771 5.1599092993 region=water
H 7.1107912923 7.8345603638 4.0663592630 region=water
O 0.7533404455 10.3823144248 9.7427261632 region=water
H 0.4650121764 10.3633312494 8.8125842599 region=water
H 1.6281143048 10.8260324856 9.7935765271 region=water
O 7.4992772454 0.3311486594 6.9546825404 region=water
H 6.6532692664 0.2672924706 7.3987235187 region=water
H 7.9595940823 10.4764733021 7.3432779021 region=water
O 7.5049398436 4.5234665399 5.0379397315 region=water
H 7.0684556847 5.4381120761 4.8947145303 region=water
H 6.8679260520 3.9572503921 4.6156654534 region=water
O 9.8587041110 6.3109465867 4.7109640612 region=water
H 8.8786870446 6.3810705292 4.7573683059 region=water
H 10.0254163481 6.0318177785 3.7828725320 region=water
O 5.3143973483 6.0072970761 0.1138972583 region=water
H 5.0255579673 5.3009555607 10.3880176563 region=water
H 6.1847221502 5.9816281098 10.8204338412 region=water
O 4.4207354749 4.8193741898 8.1507310476 region=water
H 4.8869367355 4.0141223720 7.8395890226 region=water
H 5.0807332919 5.4365017331 8.3421742844 region=water
O 3.9835117020 3.2739364021 1.4883230104 region=water
H 3.0761195668 2.9885308015 1.4915629239 region=water
H 4.1711116603 3.6194841387 2.3851094133 region=water
O 5.3166828453 9.5247935287 9.8705840482 region=water
H 6.2446088337 9.6020771029 9.7973146635 region=water
H 5.1327468977 9.8541118413 10.6846817993 region=water
O 4.1873438677 10.1602334992 1.8143293613 region=water
H 3.6217726229 10.0772794723 2.5549778031 region=water
H 3.8169669977 10.9349600269 1.2846401227 region=water
O 9.6447176054 3.7702774727 9.2504975887 region=water
H 8.6775706497 3.6384757669 8.9861295228 region=water
H 9.9242705582 2.8533701573 9.2537130195 region=water
O 9.2579317192 8.4747252196 1.6111985546 region=water
H 10.0748570043 9.0406796525 1.8293861691 region=water
H 8.4728972249 8.9540389543 2.0744391399 region=water
O 1.9162698279 3.1581882279 7.4602035020 region=water
H 1.9165126284 2.4606205687 6.6949768586 region=water
H 2.7968670220 3.6277978518 7.3731828406 region=water
O 8.4114825203 0.3991454359 1.5828322116 region=water
H 8.6975042203 0.5560304716 2.5190919144 region=water
H 7.6554794629 0.8486811716 1.2574784473 region=water
O 5.0047081847 9.8063546545 7.0944026875 region=water
H 4.8294041458 8.8735790759 7.3706995633 region=water
H 4.9462438706 10.3384960956 7.8748275535 region=water
O 3.5903153089 7.4227550972 7.2234764609 region=water
H 2.7902301448 7.5555544434 7.8782447984 region=water
H 3.8686305627 6.4829017091 7.3981033479 region=water
O 2.7820717394 1.6586452429 9.3915907869 region=water
H 2.2567023980 2.1360746814 8.6142552129 region=water
H 3.7681133628 1.6483541078 9.0423802594 region=water
O 8.3648308972 3.9663487737 1.4182441689 region=water
H 8.3853902235 4.4602240784 0.6051983957 region=water
H 8.1715205220 3.0622640154 1.1039848412 region=water
O 9.6540740930 9.6664302628 7.2942938317 region=water
H 10.2247931744 9.0920843135 6.7793638926 region=water
H 9.3293064006 9.0294366909 8.0132755599 region=water
O 10.7859733915 6.2390194036 1.8765813201 region=water
H 10.1574140218 6.9453317698 1.8723605098 region=water
H 0.0113414052 5.8956922900 0.9726808903 region=water
O 0.4608979749 8.2881005287 5.6934576381 region=water
H 0.8476920463 7.8414082519 6.4246610070 region=water
H 10.9116526571 7.5714527508 5.1915539115 region=water
O 8.1944663753 9.3384052457 9.9329467890 region=water
H 8.3802833450 8.7694273239 10.7016145864 region=water
H 8.2447730486 10.2405759765 10.3267451141 region=water
O 10.0176651568 2.8451320412 3.3668267442 region=water
H 10.0062180241 3.1604865196 4.3445485266 region=water
H 9.3169150692 3.3642024623 2.9065088768 region=water
O 1.3865550264 7.6417094016 8.7399321004 region=water
H 1.5452636547 8.3847241515 9.3703646450 region=water
H 1.2873547095 6.8765587664 9.4192707743 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0 0 1 0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0 0 -1 0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0 1 0 0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0 0 0 1
41 42 1.0
41 43 1.0 0 -1 0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0 0 -1 0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0 0 0 -1
74 76 1.0 0 0 -1
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0 1 0 0
119 120 1.0
119 121 1.0 -1 0 0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 40 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_040ps
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_035ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 80000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_035ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.9467323558 9.3891863815 3.5139264636 region=glycine
C 3.7319360940 10.6547735883 3.6393365036 region=glycine
C 4.4763165504 10.7917821436 4.9551762638 region=glycine
O 5.0788557114 0.8311536595 5.1960594496 region=glycine
O 4.5352567397 9.6698846185 5.8058960970 region=glycine
H 3.5388636878 8.4858679238 3.4048626772 region=glycine
H 2.0304429993 9.3040147347 4.0111121047 region=glycine
H 3.0598831485 0.6003497455 3.4780659380 region=glycine
H 4.6033679460 10.6067142754 2.8954351903 region=glycine
H 3.9160735496 9.0570321268 5.4009821131 region=glycine
O 2.7323949466 4.8741481904 2.3861075000 region=water
H 1.9124368212 5.2440532579 2.0962377588 region=water
H 3.5353826195 5.5560556524 2.2714624632 region=water
O 1.4939729522 2.7405079271 9.0753135671 region=water
H 1.7630633923 2.8812280412 8.1146114428 region=water
H 2.1723533022 3.1353381532 9.5698467199 region=water
O 10.8334084076 6.3179508679 5.4583234553 region=water
H 9.9575700004 5.8743626957 5.1250246164 region=water
H 10.6414985641 7.2807809996 5.5284966204 region=water
O 1.4563564892 10.3623902526 0.7396701434 region=water
H 1.9979395669 9.9901805319 1.4087612084 region=water
H 1.4580729528 0.2723038875 1.0466711147 region=water
O 10.8030863228 7.2920497708 2.0461899418 region=water
H 0.1253012404 7.9175655910 2.6558347822 region=water
H 9.8480451571 7.1316802024 2.3427583245 region=water
O 5.1460997788 1.3933957642 9.6580719641 region=water
H 5.5206312223 1.8376831761 8.8627947058 region=water
H 4.7834937710 2.2297171422 10.1364227068 region=water
O 10.2275213148 1.4502575179 4.0621198280 region=water
H 9.6401765437 2.0635130536 3.5688078549 region=water
H 10.2822209381 1.7900121089 4.9507885117 region=water
O 10.4051238140 5.0020425793 8.7068099781 region=water
H 10.2163615680 6.0044706108 8.5148058997 region=water
H 10.8051698818 5.0158400993 9.6427983228 region=water
O 4.4424344026 9.1129236864 9.0894540945 region=water
H 5.1731440647 8.5014829805 9.0069967719 region=water
H 4.9518320769 9.8713378645 8.6766050066 region=water
O 2.1255075972 2.8362630533 6.1272092437 region=water
H 1.2027811459 2.8842308378 5.8885280590 region=water
H 2.3885008649 1.8830799472 5.9689535527 region=water
O 6.2828173125 0.2498211490 2.0786116608 region=water
H 7.0539563640 0.2279925382 1.5303967916 region=water
H 6.1339166918 1.1594644989 2.4907126239 region=water
O 7.4058755328 8.0366946075 8.9927260250 region=water
H 7.5224813867 8.4321587151 8.1583891584 region=water
H 8.2601319977 7.5863698713 9.1481255944 region=water
O 0.9077192005 2.1655858964 1.1534447162 region=water
H 0.4374949304 2.1085245097 0.3576723247 region=water
H 0.8683083417 3.1383951474 1.2528292546 region=water
O 3.1947644462 6.2728867190 8.4574703275 region=water
H 2.9949054853 6.5251726345 7.4716752803 region=water
H 2.6986477661 6.9362173349 9.0620116268 region=water
O 6.2649109053 6.2405157688 4.8940502142 region=water
H 6.6010534338 6.3789105358 5.8619345782 region=water
H 5.6410749976 5.5687450289 5.0396107183 region=water
O 2.9318199155 6.9290732509 5.7083719643 region=water
H 2.0043922837 6.8767887860 5.5816692600 region=water
H 3.2009220866 5.9973321205 5.7338179324 region=water
O 7.6857772173 9.2307014411 6.5542510143 region=water
H 8.3499414435 9.4085539237 5.9534407095 region=water
H 6.8690986070 9.4884063048 6.0621009853 region=water
O 10.0995152192 7.5892493350 8.9048470952 region=water
H 10.5867647440 7.9538509203 8.1072417074 region=water
H 10.7540046577 7.3971446296 9.5844232198 region=water
O 8.7161988560 10.7477619476 0.8681175514 region=water
H 8.5433768321 10.2686773273 0.0329027419 region=water
H 8.8010273793 0.7388237286 0.6730782823 region=water
O 8.8052819738 4.9009596012 4.4284606987 region=water
H 9.0794535127 4.5914823906 3.5568377501 region=water
H 8.2658484655 5.6771729899 4.2402082324 region=water
O 5.8511539544 6.0212915850 7.9746758433 region=water
H 6.3011389557 6.6311678990 8.5372007237 region=water
H 4.8767294330 6.0037511977 8.2496632541 region=water
O 4.5630051090 7.1675901500 2.5297879744 region=water
H 5.3665270258 7.4368809577 2.0663171911 region=water
H 4.9680867941 6.7891958555 3.3343214574 region=water
O 6.3673931234 2.7520912388 7.0884465246 region=water
H 6.2209483803 3.7067193413 7.0878989340 region=water
H 6.1792806920 2.2976745343 6.2583188982 region=water
O 4.9293471129 2.5363233172 2.8892902624 region=water
H 4.0769165209 2.9316913653 2.7288998327 region=water
H 4.7480212464 2.0228388691 3.6879791111 region=water
O 3.9194224936 4.0070945916 10.4819565343 region=water
H 3.2983338216 4.4217419959 0.1934522617 region=water
H 3.9014389173 4.6947024159 9.8386661144 region=water
O 1.7923629755 8.0558711478 9.9337560154 region=water
H 1.4636452936 8.5876532918 10.7000021553 region=water
H 2.5689976405 8.5613801918 9.7111263503 region=water
O 8.3139512115 2.3840880730 0.2113606250 region=water
H 7.6011526672 3.0223275434 0.0129066867 region=water
H 8.6074229900 2.0507026286 10.2684623327 region=water
O 8.4267196780 7.3926214922 3.0600661183 region=water
H 8.6783101811 8.1563569014 3.6140956170 region=water
H 7.8511959072 7.9616459907 2.4058788888 region=water
O 1.8599476874 0.2608305585 6.4927516191 region=water
H 1.3939184917 0.3045361368 7.3626169583 region=water
H 2.4007167404 10.4012466633 6.6294734662 region=water
O 6.5642745464 8.5771353374 0.9219655776 region=water
H 6.4288278861 9.4699436233 0.8119170687 region=water
H 6.6791230941 8.1834071910 0.0693289076 region=water
O 8.5718362703 0.9317703883 8.9102642075 region=water
H 9.5656272719 0.6738526128 8.9428468730 region=water
H 8.3798139298 1.2199251756 8.0482410172 region=water
O 4.0795883160 4.5583269982 4.9264095614 region=water
H 3.5091985305 3.9335030032 5.4546987013 region=water
H 3.9872068522 4.2789641148 4.0252718181 region=water
O 0.5658106146 0.2906610724 9.1443297335 region=water
H 0.8116005134 1.2426743477 8.9531892115 region=water
H 1.2421354258 10.9024972486 9.7075709870 region=water
O 6.2377949982 4.1418588541 0.7646585317 region=water
H 5.9788432236 3.7224873280 1.5795762119 region=water
H 5.4977749061 4.0211478732 0.0323403936 region=water
O 10.3521449203 3.2195098371 6.2367101534 region=water
H 10.4092077845 3.6450077981 7.1014038849 region=water
H 10.2802126154 4.0199073113 5.6832831930 region=water
O 0.3572083699 5.1335725466 0.2808417299 region=water
H 0.6631864609 5.9209295648 0.5342258164 region=water
H 10.4935816832 4.9482382482 0.8376220949 region=water
O 0.3115217951 9.5309838584 3.9237552853 region=water
H 0.3449288753 10.4252756766 3.6366408487 region=water
H 10.7193322565 9.7614739311 4.6934091923 region=water
O 8.2909817171 10.5816822049 4.1134051811 region=water
H 9.0931131917 0.1728649047 4.0322826317 region=water
H 7.7439590591 10.8631040212 3.4047573998 region=water
O 9.7037941697 3.7757215912 2.0324129436 region=water
H 8.9796791813 3.4140310125 1.3942342252 region=water
H 10.3557009340 3.0058570347 2.2095199519 region=water
O 10.9118680734 9.0446131293 6.7080266488 region=water
H 10.8397491656 9.8941670891 7.0971055584 region=water
H 0.8365462893 8.8475291635 6.7552119821 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0 0 1 0
2 9 1.0
3 4 2.0 0 1 0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0 0 1 0
23 24 1.0 1 0 0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0 0 1 0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0 0 0 1
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0 0 0 -1
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0 0 -1 0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0 0 -1 0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0 -1 0 0
119 120 1.0
119 121 1.0 -1 0 0
122 123 1.0 0 1 0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0 1 0 0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Equilibration, cumulative 45 ps¶
Provenance: /home/ubuntu/work/02-equilibration_workdir/eq_045ps
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_040ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 90000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_040ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 5.1028097341 7.7496697663 5.2917141543 region=glycine
C 4.8048772333 9.1814028583 4.9060392250 region=glycine
C 3.5379981355 9.9018993179 5.5096196540 region=glycine
O 3.2612843685 10.9501080879 5.0592159958 region=glycine
O 2.9515141751 9.2894941732 6.6222663159 region=glycine
H 5.5660467912 7.1809231042 4.5317382561 region=glycine
H 4.2814631350 7.3379944540 5.6924151909 region=glycine
H 4.8519786018 9.2051886972 3.7792580016 region=glycine
H 5.7666582426 9.7629576751 5.2215327763 region=glycine
H 3.3451124374 8.4791711957 6.6581942103 region=glycine
O 4.7783041050 5.7378643876 1.7879345155 region=water
H 5.4276399709 6.0880132432 2.4824673347 region=water
H 4.9613326187 4.8430753192 1.7705836259 region=water
O 1.3139492092 3.3512065067 9.3120556524 region=water
H 0.6479464707 3.5101194967 8.6257880624 region=water
H 1.4888691198 4.2701440528 9.6156078108 region=water
O 2.0454164422 8.0333720714 3.6193273929 region=water
H 2.0876913498 7.4638057466 2.7921838760 region=water
H 1.8273426974 8.9432366381 3.4349813722 region=water
O 2.6315649488 1.1715710301 1.6940249248 region=water
H 2.6753456932 0.7993466491 2.5702394733 region=water
H 2.8849184612 2.1173921388 1.9407560514 region=water
O 2.4159794115 9.8252425416 10.8524509773 region=water
H 2.2253848880 10.1465978470 9.8930938105 region=water
H 2.4206634060 10.6520886587 0.4719266963 region=water
O 2.3351532747 3.4490272141 3.4694210429 region=water
H 1.6121597254 2.7860904651 3.6108556406 region=water
H 2.9064821288 3.2669293024 4.2091461871 region=water
O 0.1434237500 2.0350333754 0.4496778241 region=water
H 0.8455126477 1.6104546165 0.9725500453 region=water
H 0.5747316581 2.7826107244 10.9656806587 region=water
O 6.7528061597 8.2099229520 10.4367531395 region=water
H 5.9876164785 8.0136006280 9.9151920231 region=water
H 6.7958767708 7.3463008766 10.8452077581 region=water
O 8.3552806373 10.3006715494 9.7975186814 region=water
H 8.7403375754 10.2728234568 8.8983211058 region=water
H 7.6462789798 9.6312931051 9.8373422578 region=water
O 8.2549038417 2.2341480373 7.8990433385 region=water
H 8.6015490185 1.3424411233 8.0592793646 region=water
H 8.7380237859 2.5603969345 7.1411309689 region=water
O 5.4110202808 9.7016329181 1.8954747792 region=water
H 5.4019207529 10.4913843122 1.3210217029 region=water
H 6.0119912049 9.0644971284 1.3819726919 region=water
O 7.5625365551 3.5781918821 10.2396987951 region=water
H 6.9435311074 2.9307415744 10.5640372454 region=water
H 7.8135191597 3.2985070025 9.3430191125 region=water
O 8.0799242395 4.2771428344 2.0361165444 region=water
H 7.8510399977 5.0734008537 2.4958596451 region=water
H 8.5787093692 4.5225101925 1.2696859144 region=water
O 9.4801730335 5.6436731375 10.7756965354 region=water
H 8.7250718732 5.0912451275 10.4084906560 region=water
H 9.7847612890 6.3703215108 10.1636207612 region=water
O 3.6913242820 3.2228011803 6.0475006230 region=water
H 3.0737471392 2.8657943656 6.6502428016 region=water
H 4.0705315113 3.9875747278 6.4863377585 region=water
O 0.0409938244 6.6362092206 4.7912972155 region=water
H 0.6323728266 7.1933438834 4.3932658360 region=water
H 10.4443295261 6.4197962445 4.0132990289 region=water
O 6.9448250574 6.7362363209 7.5045385744 region=water
H 6.3743995699 7.3439917232 6.9751475226 region=water
H 7.4858019192 6.3282520026 6.7539184621 region=water
O 8.8124164380 8.7701381842 3.5729852075 region=water
H 9.4256150078 8.1708365203 3.2419994713 region=water
H 8.6393385965 9.3807654639 2.8656938219 region=water
O 10.1656125236 10.8983022315 6.9935363874 region=water
H 10.7913149396 10.8041428986 7.7742189073 region=water
H 9.8649587511 9.9956671586 6.6328737716 region=water
O 10.8860602986 5.0995005610 7.0348912164 region=water
H 10.6889701715 4.3000432730 6.4914619432 region=water
H 0.2765420545 5.7474024397 6.4004443631 region=water
O 5.0172466575 5.1064174808 8.4807385461 region=water
H 4.7562143414 5.6641431746 9.1898183514 region=water
H 5.8759281680 5.6052146572 8.1192795929 region=water
O 9.3133268235 10.5554956447 1.3406211922 region=water
H 8.8447901038 10.3306793974 0.5402022273 region=water
H 9.6416573050 0.4178065612 1.1726673476 region=water
O 6.5671728630 2.1061405531 3.1723294924 region=water
H 6.3027681315 1.4049914530 2.5755470043 region=water
H 7.1357191051 2.7520682813 2.7513747415 region=water
O 6.9179924897 6.8129548983 3.4080827267 region=water
H 7.1160217395 6.2449311229 4.0716088510 region=water
H 7.2500438737 7.6548500740 3.7150633081 region=water
O 4.2638425209 3.6216759296 10.6734058583 region=water
H 3.4518783932 4.1222814850 10.6012714100 region=water
H 4.5905525215 3.3798681324 9.7857474774 region=water
O 1.8815430216 5.8270202214 10.5008600711 region=water
H 1.2301846928 6.4674094130 10.3998859829 region=water
H 2.5312364072 5.9744916251 9.8484543359 region=water
O 10.2506738564 6.5767209214 2.1922270185 region=water
H 10.0319918140 6.0163747782 1.4105264298 region=water
H 0.2402779045 6.5454888738 2.2710202288 region=water
O 0.4626462930 10.3234801818 3.2533116455 region=water
H 0.3035874603 10.8776551787 4.0080610538 region=water
H 10.5263466966 10.1482534878 2.9555678954 region=water
O 0.7367780693 1.5517807215 5.1533730232 region=water
H 0.1481868133 1.1009219724 5.7561045839 region=water
H 1.6157054732 1.0977227096 5.2401781555 region=water
O 4.0288829682 7.3972121389 10.4046705121 region=water
H 3.6413415988 8.2689147844 10.6417954668 region=water
H 4.2309039046 6.9811653376 0.2398736880 region=water
O 5.4631629593 1.8344539149 8.3622958278 region=water
H 6.2549985063 2.3924743294 8.2305581723 region=water
H 5.2271874574 1.4257692469 7.5357358714 region=water
O 9.4807851056 3.1258831786 4.9119210128 region=water
H 10.0230102994 2.3424225471 4.8508850348 region=water
H 9.2275382605 3.3512008800 4.0136670566 region=water
O 0.2820689819 8.0062464840 9.6878547319 region=water
H 0.7821481157 8.7677748469 9.8404581067 region=water
H 0.3058841488 7.9255809141 8.7193440848 region=water
O 1.3489396119 10.8865341728 8.6564618840 region=water
H 1.8154283896 10.5943117282 7.8458204470 region=water
H 1.7363766932 0.7452875805 8.7645674581 region=water
O 8.3261627900 5.5289042093 5.5450871266 region=water
H 9.1750950627 5.9823255017 5.5362236756 region=water
H 8.5150763152 4.5873416461 5.6771390157 region=water
O 2.0905625816 5.8740661692 2.3231295411 region=water
H 2.0894195724 5.1350967465 2.9843843597 region=water
H 3.1076096521 5.8820555123 2.0217955427 region=water
O 3.2244527175 6.4937764233 6.8191894368 region=water
H 3.7253666555 5.9435797123 7.4247875709 region=water
H 2.4510333056 5.9447083436 6.4242680463 region=water
O 6.6885200504 0.4489294273 5.5628953545 region=water
H 6.9104045196 1.1227646210 4.9526389967 region=water
H 7.0264116746 0.8888151127 6.4386791465 region=water
O 5.9745704408 1.0777394919 0.2145466917 region=water
H 6.7140712247 0.7163696680 10.6824243116 region=water
H 5.4324425148 1.4254207028 10.5089661915 region=water
O 9.9981751760 8.1510227948 6.9821390367 region=water
H 9.1392088779 7.6616941456 7.2124461231 region=water
H 10.2543315015 7.6839381750 6.1410170459 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0 0 0 1
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0 0 0 -1
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0 -1 0 0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0 1 0 0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0 0 1 0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0 1 0 0
92 93 1.0
92 94 1.0 -1 0 0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0 0 0 1
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0 0 1 0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0 0 0 -1
125 127 1.0 0 0 -1
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Production, cumulative 100 ps¶
Provenance: /home/ubuntu/work/03-production_workdir/prod_100ps
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
InitialVelocities
File /home/ubuntu/work/02-equilibration_workdir/eq_045ps/ams.rkf
Type FromFile
End
NSteps 200000
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 4.4061911919 6.6382997924 4.6818611363 region=glycine
C 2.9011537651 6.5068497391 4.6001692807 region=glycine
C 2.1844267672 6.6689424639 5.9431904526 region=glycine
O 1.0608395049 6.9931581733 5.9236623627 region=glycine
O 2.8659301808 6.2298745091 7.0450067738 region=glycine
H 4.9643151681 6.5950468929 3.8064605126 region=glycine
H 4.9093307654 5.9961781259 5.3647451961 region=glycine
H 2.6633648502 5.4772084251 4.0891965463 region=glycine
H 2.6316642921 7.3571776626 3.8755224204 region=glycine
H 3.7649636441 5.8786523529 6.7080338471 region=glycine
O 7.2248321700 1.0971813073 9.5466409094 region=water
H 6.4619604764 0.6635533108 9.1812986813 region=water
H 6.8978869139 1.9070052837 9.9087475165 region=water
O 10.2356875898 3.4526585220 0.0978747076 region=water
H 0.1427643305 3.2384931756 10.8235976375 region=water
H 10.1403807752 4.4313051429 10.9443398769 region=water
O 10.7084252191 9.6544699547 4.1862413312 region=water
H 10.7681240440 10.5088789465 3.7143472287 region=water
H 9.7181834997 9.4121245626 3.9960743735 region=water
O 10.6898422162 6.6909961589 10.4108905996 region=water
H 10.5602848583 6.9378122582 9.5146506949 region=water
H 0.5866754246 7.1130936560 10.6877440943 region=water
O 1.3662642589 0.5236663950 1.2351801097 region=water
H 2.0815404227 0.0383536250 1.5227614828 region=water
H 0.5733444170 10.9542192482 1.1661618513 region=water
O 5.8337584358 1.3338983976 6.7744035222 region=water
H 6.4388337868 1.2690403356 6.0690348136 region=water
H 5.8838357387 0.4290942861 7.1206941984 region=water
O 9.3561908371 2.7163488381 2.5101730841 region=water
H 8.3583611699 2.9615254469 2.4036883395 region=water
H 9.6969224188 2.6670464489 1.6445871982 region=water
O 6.5571299184 2.8420332696 2.1093299384 region=water
H 6.7645918262 1.9717853192 1.7841406979 region=water
H 6.5127897955 3.3952736268 1.2854016687 region=water
O 8.2825622033 7.4200473000 5.7895609281 region=water
H 8.9699431126 7.4465287230 6.4797779371 region=water
H 7.5388838102 7.9974687846 6.2123756184 region=water
O 1.2760834370 2.8662278413 5.9950004260 region=water
H 0.8791436997 2.6421916973 5.1190250191 region=water
H 2.2203608259 3.2273186660 5.8269558867 region=water
O 4.9817811109 9.8735233434 4.3201879608 region=water
H 4.0646126402 9.9627307351 4.6951367213 region=water
H 5.4051931988 10.7763014896 4.3286630705 region=water
O 5.0253692900 10.3723015586 8.8476434622 region=water
H 4.1523780437 10.4871323204 8.5426827511 region=water
H 5.4644606694 9.7300706932 8.2476402135 region=water
O 6.3772433821 6.2256730393 9.7246478566 region=water
H 7.0943240212 5.6193372192 9.9190669301 region=water
H 6.2213799606 6.2131343374 8.7526169876 region=water
O 9.5210862586 10.1649727241 0.6905795289 region=water
H 8.6626678149 9.9999331237 0.3139096059 region=water
H 9.4888147109 9.6418614053 1.4864686579 region=water
O 9.4530154638 4.1422534846 6.0042492975 region=water
H 9.4595599096 4.8012742040 5.3538427560 region=water
H 10.3422327925 3.8492400991 6.0480774337 region=water
O 1.5724269709 8.4472294058 2.6357690841 region=water
H 1.4592611371 8.3942479483 1.6882433985 region=water
H 0.7056592888 8.7511681101 2.9698797133 region=water
O 8.4200962649 8.6345449606 3.2539641877 region=water
H 8.5914210775 7.9104426865 2.4923653209 region=water
H 7.9241053529 8.1588951697 3.9264344928 region=water
O 6.5472565036 0.1394831269 1.7225998587 region=water
H 6.1741097992 10.8400249490 2.5696985199 region=water
H 6.8273496798 10.3689908163 1.1261102967 region=water
O 2.6434970719 9.8337524848 7.6922235261 region=water
H 2.2076789251 10.1017797523 6.8929110680 region=water
H 1.8443403373 9.5032563578 8.2193255372 region=water
O 3.8669323998 3.0655484360 5.5866514863 region=water
H 4.4190829766 2.6375145241 6.2836401159 region=water
H 3.9101005763 2.5062178496 4.7980938509 region=water
O 5.4722398514 3.2342651971 10.5771267588 region=water
H 4.5238474085 3.3447374291 10.8725107960 region=water
H 5.7064429567 4.2311995110 10.5734046355 region=water
O 7.5533121647 0.0651571925 4.7584941205 region=water
H 8.4960783961 10.9676233474 4.8647829348 region=water
H 7.2428042440 10.5107913824 4.0705273364 region=water
O 4.1174946225 1.4390880672 3.2118982318 region=water
H 5.0306156544 1.6704604136 3.0223966865 region=water
H 4.1873389593 0.5289169004 2.9671666464 region=water
O 6.0107602852 6.2954893781 2.2540993784 region=water
H 6.8364555114 6.3589172875 1.8341548531 region=water
H 5.4049979972 6.2625655543 1.4780024343 region=water
O 1.8139243293 1.5481575667 8.9251930696 region=water
H 1.5537441553 0.6157901931 8.6666546060 region=water
H 1.8055074367 1.9242936379 7.9857564249 region=water
O 3.8526105160 6.0034374235 10.8091282767 region=water
H 4.7833367307 5.9149530586 10.4004189476 region=water
H 3.1783771293 5.3782527996 10.4747606186 region=water
O 8.8152337242 6.5227579426 1.3549909026 region=water
H 9.5742983632 6.6967114576 0.6183862375 region=water
H 9.2750000160 6.3636561546 2.2618434444 region=water
O 2.3105235603 10.4699940571 5.1961802402 region=water
H 1.8223280964 9.8488406783 4.6023933826 region=water
H 1.8996056310 0.3162590353 4.9787726168 region=water
O 2.4147730888 3.3309672894 0.2179026166 region=water
H 2.2066600743 2.9619296425 10.3016611177 region=water
H 2.4656612427 2.5670787604 0.7820299141 region=water
O 2.0714629997 8.0701191564 10.7501900204 region=water
H 2.5616826958 8.9372724156 10.8739492235 region=water
H 2.6958305479 7.3771735155 10.6320089398 region=water
O 7.0053511196 8.9047218716 10.7162309306 region=water
H 6.4833980559 9.1629150299 9.8847620248 region=water
H 7.0487810076 7.8962460834 10.6285045160 region=water
O 0.6077873213 1.7328457566 3.5968861478 region=water
H 10.8018920722 2.3253091583 3.5055684221 region=water
H 0.9021022073 1.3621553974 2.7079785054 region=water
O 10.1392144586 7.4850616289 7.6713968975 region=water
H 10.5525802597 8.2606645586 8.0848313100 region=water
H 10.8076316543 7.0746664260 6.9601202768 region=water
O 10.8420467466 9.8932866562 8.9511787679 region=water
H 10.4277720633 10.4108767633 8.3103517365 region=water
H 10.2908746330 9.8529879084 9.8160096177 region=water
O 9.9309364562 6.0623718415 3.8979818559 region=water
H 9.4296031178 6.7537456890 4.2736328627 region=water
H 10.8753257794 6.2878414385 3.8872421776 region=water
O 2.1908837623 4.4990860759 2.4816901365 region=water
H 2.3542708980 4.5767039470 1.4976344283 region=water
H 2.1469210043 3.5970155148 2.7112959446 region=water
O 5.9109944360 5.5373372647 6.7952995710 region=water
H 5.8849933137 4.6092591807 6.7444276850 region=water
H 6.7709584141 5.7864076275 6.5609136066 region=water
O 6.1150596865 8.7462044579 6.9006673539 region=water
H 5.7096698078 9.2276049907 6.1214861302 region=water
H 5.8401049204 7.8307632477 6.6637554054 region=water
O 3.5203795919 10.3396912488 0.1518181652 region=water
H 4.2386238158 10.5727932838 10.4922441630 region=water
H 2.8187299231 10.9181701478 10.8755554718 region=water
O 9.1777802430 0.5183149149 7.1102577778 region=water
H 8.5285110835 0.5660986913 6.4805242314 region=water
H 8.6707967387 0.6064705859 7.8993773507 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0 1 0 -1
14 16 1.0 0 0 -1
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0 1 0 0
23 24 1.0
23 25 1.0 0 -1 0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0 0 -1 0
62 64 1.0 0 -1 0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0 0 -1 0
74 76 1.0 0 -1 0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0 0 1 0
95 96 1.0 0 0 -1
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0 -1 0 0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0 0 0 -1
125 127 1.0 0 0 -1
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Production, cumulative 150 ps¶
Provenance: /home/ubuntu/work/03-production_workdir/prod_0150ps
LoadSystem
File /home/ubuntu/work/03-production_workdir/prod_100ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 300000
Restart /home/ubuntu/work/03-production_workdir/prod_100ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.8760759835 0.1088542459 7.0275643728 region=glycine
C 1.5391470307 10.6667730325 7.6106780759 region=glycine
C 0.9576985468 9.3661865042 7.0573136225 region=glycine
O 0.2191137535 8.7216094609 7.7006474106 region=glycine
O 1.3448910813 8.9938006531 5.7857149476 region=glycine
H 2.8029164563 0.4232209132 6.0546080143 region=glycine
H 3.2451149907 0.8759456645 7.5630947758 region=glycine
H 0.8004806987 0.5198694477 7.4670514552 region=glycine
H 1.5860833343 10.3089351768 8.6843151431 region=glycine
H 1.8306634705 9.7987908426 5.4724390061 region=glycine
O 3.0481751759 8.8863314294 2.5194162069 region=water
H 2.4833756051 8.5284269305 1.7493224642 region=water
H 3.8497629136 9.2371958370 2.0515990287 region=water
O 7.3661550940 9.0430684653 7.5756013870 region=water
H 7.7763787738 8.2395857800 7.2165762260 region=water
H 6.5095254906 9.1975398441 7.1368686109 region=water
O 10.2256409807 5.2478831500 5.0677714071 region=water
H 9.9516298942 5.7368397021 5.8970307827 region=water
H 0.1936605440 5.5119353361 4.8469727557 region=water
O 5.5314467251 5.4014214933 0.6050413270 region=water
H 4.8973473295 5.2235645104 1.3970446879 region=water
H 6.2630636279 5.8344128445 0.9373951351 region=water
O 4.1183765496 8.6692738681 8.6876499588 region=water
H 3.5053730239 9.2233684633 8.1379614308 region=water
H 4.9475176350 8.6847336879 8.1478807521 region=water
O 8.5474308582 5.1230802852 9.8126331947 region=water
H 7.9251368519 4.8229765980 10.4593513806 region=water
H 9.3655630457 4.7068977735 10.1807203186 region=water
O 9.8981993222 9.3993222083 10.1693046932 region=water
H 9.1393583229 9.9324842000 9.8537754428 region=water
H 10.4731904759 9.3325209186 9.4156795065 region=water
O 7.7062051012 8.1609197755 0.6881788892 region=water
H 8.5731788640 8.1842557740 0.1856145638 region=water
H 7.8237646902 7.4345858221 1.2634700422 region=water
O 5.9291869331 1.8937868620 10.8080153022 region=water
H 6.6444777550 2.5106424968 10.9434006386 region=water
H 5.7649531725 1.5884883062 0.7591332379 region=water
O 9.9783372166 2.5718925701 10.0097220914 region=water
H 9.6076868811 1.9214028859 9.4230559232 region=water
H 10.7295148640 2.1827125121 10.3975198690 region=water
O 8.3055113300 7.5121146321 5.3815007077 region=water
H 7.5495245742 7.6586137164 4.7706038842 region=water
H 8.8938464661 6.8940142615 4.9138865076 region=water
O 10.8148876016 9.6787844126 2.1234909744 region=water
H 10.8031156897 9.2993068930 1.1867839515 region=water
H 0.3980908653 10.4102696124 1.9976215060 region=water
O 8.4498358194 0.5601354506 8.3802668725 region=water
H 8.1844324793 10.6248214190 8.1495877267 region=water
H 7.6326052837 1.0700253349 8.2656836671 region=water
O 7.6300083337 5.2681715423 6.7467560923 region=water
H 8.3175379590 5.4274951291 7.3999553665 region=water
H 7.5861541720 6.0138329243 6.1481097814 region=water
O 5.0449193020 9.6241704318 0.9229044858 region=water
H 5.8578826749 9.1371130516 0.5824697880 region=water
H 4.6131141414 10.0273382579 0.1747432349 region=water
O 6.3763991972 2.3195749362 6.3188296386 region=water
H 6.6385024200 3.2479449458 6.3314834109 region=water
H 7.0570380850 2.0795481726 5.6900093624 region=water
O 4.4404943489 5.2652018523 3.2707679502 region=water
H 4.7371821385 6.1894994585 3.5645931310 region=water
H 3.5913440623 5.1492129974 3.7340580244 region=water
O 0.4747123905 6.1613861583 1.0577414204 region=water
H 0.8435958927 5.7238858965 0.3015232018 region=water
H 0.9680223677 7.0619410114 1.1618390926 region=water
O 10.8197636804 2.8409422143 3.2125763435 region=water
H 10.5569894619 3.4692415674 3.8813323798 region=water
H 10.0503225645 2.2028257659 3.1465235366 region=water
O 2.4490308554 0.1657031760 4.2751894719 region=water
H 2.4038625125 10.4524579311 3.6190825721 region=water
H 2.8206373973 0.9087657848 3.8062592285 region=water
O 5.6875181376 7.4880763125 3.7554055362 region=water
H 5.2279170868 7.9185030139 2.9788576074 region=water
H 5.2476243097 7.9363914491 4.5978528378 region=water
O 5.5793003127 2.6171007930 2.1423811926 region=water
H 4.6221893666 2.8110227462 2.0541654227 region=water
H 5.9796487944 3.4325976386 1.7329367193 region=water
O 5.4242818006 9.7307800835 5.5915274082 region=water
H 4.6488785599 10.1833039781 5.9547238467 region=water
H 5.7405658126 10.4054832231 4.9165416719 region=water
O 1.9725449923 6.0612397903 4.4786526099 region=water
H 2.2747039325 5.4251903749 5.1488652671 region=water
H 2.0601184872 6.9197378537 4.9658161518 region=water
O 9.6093507913 1.8919691605 6.3638223006 region=water
H 9.0285344348 1.6875129399 7.1356807503 region=water
H 9.4069520269 2.8488353846 6.1430732221 region=water
O 2.8092743952 2.6328170642 2.8998358314 region=water
H 1.9339214958 2.6811706150 3.2793514048 region=water
H 3.2440378322 3.4818659272 3.2240999088 region=water
O 8.7208502055 6.0720205465 2.2969285977 region=water
H 9.6313282926 6.2920993242 2.0008340377 region=water
H 8.6066099540 5.1990470374 1.8037150063 region=water
O 9.0971247021 0.7184539376 2.5443912823 region=water
H 8.2743102168 0.4099314830 2.9051156300 region=water
H 9.6940265765 10.8998932734 2.4837721672 region=water
O 0.8841929838 1.3220572198 0.8644206388 region=water
H 0.1546613914 1.2513087235 1.5137752105 region=water
H 1.6177024427 1.5759131621 1.3580510158 region=water
O 2.5818440159 0.2589946421 10.0817016527 region=water
H 2.0727201701 0.9584868508 10.5393505561 region=water
H 3.1078528928 0.7268578700 9.4803136045 region=water
O 4.7439178812 5.0822041567 7.0006815515 region=water
H 4.5902526312 5.0741890541 7.8976517311 region=water
H 5.7299669079 4.8331924712 6.9046766575 region=water
O 4.4462894505 2.0455249819 8.3891853504 region=water
H 5.1599120652 2.2169861343 8.9692298153 region=water
H 4.8093776551 1.9954960384 7.5190226781 region=water
O 2.5528975998 3.7743138808 6.0889334061 region=water
H 2.0195413178 3.4431034012 6.7348860573 region=water
H 3.2506926349 4.3156831114 6.5769691989 region=water
O 3.5767942589 5.9188977566 9.5854699420 region=water
H 4.2725207960 5.5593385317 10.2784700284 region=water
H 3.9280086918 6.8241211310 9.3593886050 region=water
O 0.7699183977 2.5684603728 7.7745894471 region=water
H 0.0589476973 2.4523581775 7.0859921480 region=water
H 0.3718767702 3.0769430906 8.4970752789 region=water
O 1.0014883500 5.0517268839 9.4932983740 region=water
H 0.6162702652 5.4332021328 8.7203007287 region=water
H 2.0032309813 5.1324772313 9.4367674504 region=water
O 8.8329867845 3.6285803657 1.1583569792 region=water
H 9.5389785598 3.3087548216 0.6809147881 region=water
H 8.8726017085 3.1594043520 1.9928126299 region=water
O 10.2892997987 6.2072044528 7.6630550281 region=water
H 9.8158247117 6.1639267796 8.5053112484 region=water
H 10.3587102998 7.2182333763 7.5112942061 region=water
O 6.3932485764 10.9576461742 3.2295814729 region=water
H 6.0791018069 0.9333066271 3.2315466262 region=water
H 5.9052154973 10.5972671349 2.5009584608 region=water
O 1.9387052566 8.3153099765 0.0298559911 region=water
H 2.5134273811 8.9723787488 10.6242484666 region=water
H 1.4195442119 8.0299529447 10.2725186316 region=water
End
BondOrders
1 2 1.0 0 -1 0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0 0 1 0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0 1 0 0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0 0 0 1
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0 1 0 0
47 48 1.0 0 -1 0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0 0 -1 0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0 0 -1 0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0 0 1 0
125 127 1.0
128 129 1.0 0 0 -1
128 130 1.0 0 0 -1
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Production, cumulative 200 ps¶
Provenance: /home/ubuntu/work/03-production_workdir/prod_0200ps
LoadSystem
File /home/ubuntu/work/03-production_workdir/prod_0150ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 400000
Restart /home/ubuntu/work/03-production_workdir/prod_0150ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 7.6733102340 3.0323997704 2.8648505490 region=glycine
C 7.0133282354 1.9267093435 3.6564610646 region=glycine
C 5.4739545738 1.9558795372 3.5192272576 region=glycine
O 4.7584926420 1.6138011915 4.3737334821 region=glycine
O 5.0174998901 2.2624507612 2.2748194725 region=glycine
H 8.7333622402 3.1496647204 2.9890009493 region=glycine
H 7.2942699050 3.9754610684 3.1716890077 region=glycine
H 7.2748282344 1.9569120128 4.7458051320 region=glycine
H 7.5091680205 1.0284867421 3.2748171060 region=glycine
H 5.8477206826 2.6122181613 1.8266907808 region=glycine
O 8.6904224549 2.1365140083 0.0562170731 region=water
H 8.3894814100 2.3554554430 0.9381929568 region=water
H 9.3986170702 1.5400225910 0.1995530990 region=water
O 3.1011023315 6.2982014048 8.5578098731 region=water
H 2.4719895117 5.6348886503 8.7290098391 region=water
H 2.6138519732 7.0963551964 8.7571652715 region=water
O 2.6662528286 9.1533885595 7.5642770901 region=water
H 3.3001192520 9.9243025758 7.4462029800 region=water
H 2.2589641642 9.0403705174 6.7488832696 region=water
O 10.5454616936 5.9742200758 9.6599334126 region=water
H 10.5533524663 5.4887287063 8.8334743156 region=water
H 10.7500145017 5.2947195662 10.3221256765 region=water
O 1.9674224049 8.2838275759 4.7320959573 region=water
H 1.7840641166 9.2314148358 4.9019782302 region=water
H 1.0989494106 7.8185147267 4.7897059070 region=water
O 9.2607260001 8.3855085304 1.3077148015 region=water
H 10.1590248506 8.8041353583 1.0993561978 region=water
H 9.1697777250 7.7186154378 0.6168519112 region=water
O 7.0754881203 0.2951040678 9.7975225389 region=water
H 6.7050194303 10.4991319159 10.2727027927 region=water
H 7.6482078579 0.8451768072 10.3510979072 region=water
O 4.7821092833 9.2161915417 9.9856840683 region=water
H 5.0012786398 9.5526485184 9.1576013494 region=water
H 5.5424355445 8.5750821434 10.1701735468 region=water
O 8.4616561596 5.4688585064 6.2250076603 region=water
H 9.4071221016 5.3180807114 6.1448444013 region=water
H 8.2097819435 5.7902278021 5.3550925707 region=water
O 2.2074309860 4.6618374747 5.0447359049 region=water
H 2.0511768545 3.8967565987 4.3970051685 region=water
H 3.1169269668 4.5004474120 5.4854669698 region=water
O 6.5181597270 9.5260996255 4.5511214134 region=water
H 7.1943199583 8.8090087224 4.6062461256 region=water
H 6.3273887413 9.7374434576 5.4789972665 region=water
O 6.6999050850 7.4325952111 7.8149437485 region=water
H 6.9283327464 6.9315294362 7.0748421029 region=water
H 7.5281660669 7.3466291864 8.4301992671 region=water
O 9.8881810738 1.1415978251 7.4770909431 region=water
H 9.7567827194 1.0602253384 8.4911923757 region=water
H 9.4300858829 1.8837855830 7.0548109830 region=water
O 10.4550818726 0.0198950271 9.7629726986 region=water
H 10.4912442238 10.4271819011 9.0212498248 region=water
H 10.7357699795 10.3545238426 10.3984883862 region=water
O 3.8915485700 9.9739264293 2.3417273877 region=water
H 4.3243571856 10.4941437694 2.9507447299 region=water
H 4.3236439568 9.0655617460 2.2055392982 region=water
O 7.4664530809 10.4419045025 7.2123395613 region=water
H 7.3848099321 10.5330092210 8.1832412452 region=water
H 7.8202660911 0.3253430989 6.9173404380 region=water
O 8.1585234935 7.1780838141 9.8680907145 region=water
H 9.1201341126 6.9346658921 9.8162409574 region=water
H 7.6972006762 6.2962496119 10.0316674847 region=water
O 4.8092813462 10.7888927845 7.2069560823 region=water
H 5.7130873226 10.3738197733 7.1140019775 region=water
H 4.7124591818 0.3971811858 6.4327231698 region=water
O 4.5977097188 7.6763749560 3.5950514738 region=water
H 3.7937649176 7.6279211083 4.1335557502 region=water
H 5.0092624005 8.4809180053 4.0117957465 region=water
O 10.2676267850 8.9196139132 7.6129235729 region=water
H 10.7761643459 9.0999740541 6.8613912501 region=water
H 9.6547648702 9.7227773700 7.3652735896 region=water
O 1.2156716693 9.8863449172 1.2009283581 region=water
H 1.3082683228 9.2328151636 0.4929932922 region=water
H 2.1003283350 9.9847872829 1.5881571471 region=water
O 4.4667176397 6.1360076974 0.0435714892 region=water
H 5.3421141132 5.7740921330 10.9617508014 region=water
H 4.3858833261 6.6625694237 10.2409770113 region=water
O 10.3508900792 2.8373314906 3.8081866633 region=water
H 9.7978235071 2.0562334019 3.6129791487 region=water
H 0.1783512277 2.8732809983 3.3032236739 region=water
O 5.3666815357 2.4274001622 8.3684310309 region=water
H 5.8291569850 1.8572047631 9.0200406728 region=water
H 4.7084697255 1.7433759111 8.0536572515 region=water
O 0.3982755028 4.8816993422 0.7811310816 region=water
H 1.1704115696 5.4787748214 0.9669909469 region=water
H 0.7620080801 4.0879609925 0.3703447848 region=water
O 9.1013561310 8.2977860075 4.0459359105 region=water
H 9.0681498631 8.3225859199 3.1081641632 region=water
H 9.4134209911 7.3481390311 4.2709957484 region=water
O 2.8637052883 3.7673658431 9.5741374944 region=water
H 3.7313588580 3.3795825617 9.3731820989 region=water
H 2.3404376200 3.0701816067 10.0862177802 region=water
O 7.8205543702 2.8637611888 6.6554726883 region=water
H 7.1289208396 2.6617949238 7.3386095611 region=water
H 7.7555513084 3.8476364125 6.5704790597 region=water
O 9.1814776862 0.2164036739 3.1982932778 region=water
H 8.9903262516 10.4319582622 3.7531838068 region=water
H 9.0665043749 10.7972794705 2.3414370601 region=water
O 6.6843978695 5.7004727365 3.9516030370 region=water
H 6.2465077078 6.5431308712 4.0045993533 region=water
H 6.0367151105 5.2944695675 4.5976314549 region=water
O 6.1077714730 8.1428808198 1.0780515346 region=water
H 6.6818317282 7.5383454108 0.6742626773 region=water
H 5.3984063441 7.5227217398 1.4452729134 region=water
O 4.6287572100 4.6489590649 6.3846742983 region=water
H 4.2571759390 4.9649949624 7.2293353660 region=water
H 4.7852149562 3.7468928936 6.5191001186 region=water
O 2.7283318816 5.9374781983 2.3357862169 region=water
H 3.2959230735 5.9132142901 3.0950985176 region=water
H 3.2357088364 6.0070078986 1.5891149504 region=water
O 1.1687869725 8.0862685068 10.0843390231 region=water
H 1.7506921858 8.5074168173 9.4389199336 region=water
H 0.6272747665 7.5716593287 9.5405965202 region=water
O 0.7528567190 10.8607031747 5.6905181944 region=water
H 0.1149038681 0.1285316063 6.3350174484 region=water
H 0.8882240694 0.6792269546 5.2301135919 region=water
O 1.9902991226 2.7255169983 2.7987054082 region=water
H 2.7464992096 2.3272294401 3.1918093128 region=water
H 2.2735476682 2.5657809741 1.8462571674 region=water
O 6.9504003463 4.5905089091 10.3518570021 region=water
H 6.2743554490 4.2035182813 9.9017047301 region=water
H 7.6432113421 3.9106586342 10.4949561057 region=water
O 10.7568885511 5.8854202635 4.4003292518 region=water
H 0.6919466891 5.7867428808 4.5998715285 region=water
H 10.6134203750 4.9676611118 4.0970324233 region=water
O 0.1144360744 4.4155946649 7.5000697349 region=water
H 10.8148935280 4.5742484635 6.5458105086 region=water
H 1.0963866209 4.4559611465 7.4856516645 region=water
O 1.4294842155 1.7949922065 0.0224753923 region=water
H 0.4955894756 1.7123513471 10.6187867222 region=water
H 1.7118710704 0.8634343532 0.1327340352 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0 0 -1 0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0 0 -1 0
50 52 1.0 0 -1 0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0 0 1 0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0 0 1 0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0 0 0 -1
74 76 1.0 0 0 -1
77 78 1.0
77 79 1.0 1 0 0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0 0 -1 0
95 97 1.0 0 -1 0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0 0 1 0
113 115 1.0 0 1 0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0 1 0 0
122 124 1.0
125 126 1.0 -1 0 0
125 127 1.0
128 129 1.0 0 0 -1
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Production, cumulative 250 ps¶
Provenance: /home/ubuntu/work/03-production_workdir/prod_0250ps
LoadSystem
File /home/ubuntu/work/03-production_workdir/prod_0200ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 500000
Restart /home/ubuntu/work/03-production_workdir/prod_0200ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 5.1814486621 7.7899107641 1.2916261363 region=glycine
C 5.7663986049 9.1465799451 1.6173863138 region=glycine
C 5.9997307297 9.3562208147 3.1243045402 region=glycine
O 6.7976029715 10.2031794327 3.4781100739 region=glycine
O 5.2628976500 8.6602437106 4.0674310133 region=glycine
H 5.8908799659 7.0143861416 1.4091370646 region=glycine
H 4.9632922706 7.7490023704 0.2270464388 region=glycine
H 5.2105742736 9.9798842431 1.1348000940 region=glycine
H 6.8983487669 9.3266108857 1.2160343301 region=glycine
H 4.7772627981 8.0126984349 3.5034547304 region=glycine
O 10.5413001698 6.4868555110 5.7312899233 region=water
H 9.9415023794 6.6956059593 4.9453289355 region=water
H 9.8854623807 5.9965895562 6.2377557177 region=water
O 10.2649469237 4.9174262593 10.8411759354 region=water
H 10.3850511733 5.6029582756 10.2056181684 region=water
H 10.4661651067 5.3052763303 0.7595057213 region=water
O 6.1089864235 5.4735098329 6.2797572534 region=water
H 5.3859389947 5.2412971728 6.8190698326 region=water
H 6.9367652287 5.1098116072 6.7241150688 region=water
O 3.6726930397 2.5245875692 5.9479599501 region=water
H 3.7512727648 3.2823333035 6.5724652026 region=water
H 3.2809933799 1.7003823874 6.3833094575 region=water
O 6.9692605648 2.3675822630 0.3645887283 region=water
H 7.7311984884 1.7615344236 0.4498881839 region=water
H 6.8541967840 2.6579362711 1.2481247681 region=water
O 4.9068625462 0.2305660312 10.6487259302 region=water
H 4.3495308758 0.2103644183 9.8560011341 region=water
H 5.3352788077 1.1882064578 10.6824964433 region=water
O 8.9299600908 4.1766445912 7.1178493869 region=water
H 9.0258657475 4.0616197871 6.1198677321 region=water
H 8.8992049824 3.2758848335 7.4694566808 region=water
O 10.5056184166 2.1632024389 3.1221210562 region=water
H 10.2268853438 1.4254657386 3.6799054174 region=water
H 0.4352082598 2.5001696205 3.5116761135 region=water
O 6.1959715133 9.5903390314 8.2002837496 region=water
H 6.1128604011 10.5525157689 8.3294575163 region=water
H 6.2485979738 9.5710954661 7.2006306707 region=water
O 0.4231819960 9.2605825647 6.4890964122 region=water
H 0.2716499664 8.3464681013 6.2835783044 region=water
H 10.6003070587 9.4630885347 7.0182168566 region=water
O 2.1244873979 8.0532759821 2.5208939672 region=water
H 3.0108613718 8.2357675910 2.4021365637 region=water
H 2.0653352120 7.5262731070 3.2999575605 region=water
O 10.0787378692 1.5745679394 0.2152010203 region=water
H 10.5378019411 1.5244051783 1.0932715025 region=water
H 10.1671370008 2.5382020189 0.0749806815 region=water
O 1.7408638182 10.9235777120 10.2115428408 region=water
H 0.9220103980 0.1111742504 10.6357216528 region=water
H 2.3299225528 10.8926961657 0.0066802392 region=water
O 8.9808251370 7.5040213528 3.3316883562 region=water
H 8.0779632029 7.7793441125 3.1559812125 region=water
H 9.4148442830 8.3635103182 3.1248683312 region=water
O 5.0620023012 7.4993009248 9.3977137782 region=water
H 5.8065413909 6.8329289457 9.1502533177 region=water
H 5.3059551163 8.2943726801 8.9006153819 region=water
O 1.1102969113 5.6419686656 1.5677007642 region=water
H 1.9279581920 5.1305378497 1.3428337802 region=water
H 1.3933213274 6.4835196694 1.9384268939 region=water
O 5.0710662157 5.8596910493 3.7630633570 region=water
H 4.1470222835 5.7971839671 4.0377295474 region=water
H 5.5774422587 6.1036912276 4.6002129763 region=water
O 8.3311959570 10.1160644993 0.2612260809 region=water
H 8.9094013540 9.6539589908 0.9245573746 region=water
H 8.7957714424 0.0441601883 0.1574831532 region=water
O 9.5605660241 1.7474712454 8.3402686519 region=water
H 9.4205604843 0.7900068655 8.2790143916 region=water
H 9.9891952742 1.8620353799 9.2139520357 region=water
O 3.8720606165 4.2066225566 1.2110568819 region=water
H 4.7929352269 4.3798716889 1.5751218067 region=water
H 3.6087900726 3.3260244874 1.5606878404 region=water
O 1.0309374101 4.2933240614 8.2595878528 region=water
H 0.3639996329 4.1495095802 7.5327514464 region=water
H 0.4301262254 4.1450698472 8.9832660035 region=water
O 8.9810664498 4.1791909024 3.9131240493 region=water
H 9.1225279360 5.1189853195 3.7488012015 region=water
H 9.7735704742 3.6559490020 3.5904360802 region=water
O 4.7296157335 3.0232779565 9.9187118490 region=water
H 4.2974196087 3.6581615545 10.4819000275 region=water
H 5.7249115784 3.0021165066 10.1707972040 region=water
O 1.9319906164 7.7530889116 10.1524119602 region=water
H 1.7169095616 8.3647764151 10.8520549905 region=water
H 2.9493241850 7.7656737453 10.1148832336 region=water
O 6.5379506657 1.2080484749 7.8976366312 region=water
H 5.9983555517 1.6671968788 8.5412308727 region=water
H 7.4370214647 1.2153744805 8.2921131870 region=water
O 7.5658296656 5.7185629590 9.0969117888 region=water
H 7.9868173776 5.2898084038 8.3203711130 region=water
H 8.3510894565 6.2357334849 9.4099991025 region=water
O 2.1930045926 0.4289629048 7.1323847741 region=water
H 1.2380001715 0.1559647917 7.0086930738 region=water
H 2.3246918094 0.1623653454 8.1013551857 region=water
O 0.4698956501 10.9204665214 4.3225890458 region=water
H 0.6195426034 10.3444943596 5.1527536303 region=water
H 1.3243259284 10.9218177896 3.9518022047 region=water
O 10.2027433455 6.9605035216 8.7760945370 region=water
H 0.0583505249 7.2857133620 9.0975282639 region=water
H 10.4985288656 6.7291435519 7.8772187958 region=water
O 6.5897812256 5.3683341946 0.9456422810 region=water
H 6.7526596141 4.3970596989 1.1584879824 region=water
H 6.6558245104 5.4158586245 10.9603720650 region=water
O 2.4545287867 7.0376975408 5.1348540331 region=water
H 2.9601086960 7.6367612550 5.7182782382 region=water
H 1.5452933291 6.9784235691 5.4853610999 region=water
O 2.0716543961 3.0899480867 3.7231134269 region=water
H 2.7855503767 3.3356645098 3.0932251170 region=water
H 2.6940022326 2.9688541383 4.5618917337 region=water
O 6.2166313819 3.3928511003 3.5417637690 region=water
H 5.8685139310 4.2064711629 3.8936775771 region=water
H 7.2015519175 3.4339202846 3.4613169512 region=water
O 3.8120494709 8.9452137440 6.4453935590 region=water
H 4.3621666303 9.2597945490 5.7771741490 region=water
H 3.0412202721 9.5688215718 6.4752081339 region=water
O 8.9223159165 10.0510503418 8.4979612222 region=water
H 8.6876586212 9.8573326301 9.4281030569 region=water
H 8.0782938153 10.0737765524 8.0520178887 region=water
O 2.2086866602 0.4575366793 1.8603980911 region=water
H 2.7074405015 0.9170915286 2.5643863319 region=water
H 1.9449019090 10.6146598169 2.1989064344 region=water
O 3.7942526458 4.4013683386 7.6926555971 region=water
H 2.8019556823 4.4516703106 8.0538647583 region=water
H 4.2797472942 3.9292516279 8.4037455356 region=water
O 10.5839763961 9.6600871218 2.1047732424 region=water
H 0.1890294672 8.8503393773 2.1726331448 region=water
H 10.3896992409 10.0542858735 2.9942194997 region=water
O 4.2719055494 1.6354042019 3.2554358570 region=water
H 4.4992624119 1.6612851638 4.2258813340 region=water
H 5.0449911400 2.0950006142 2.8397138563 region=water
O 7.4600438154 10.0110540827 6.0828914016 region=water
H 7.9357661541 10.8809938929 6.1586539038 region=water
H 6.8944955680 10.0916816812 5.2309765492 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0 0 0 1
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0 1 0 0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0 -1 0 0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0 0 1 0
47 49 1.0 0 0 1
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0 0 1 0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0 1 0 0
95 97 1.0
98 99 1.0
98 100 1.0 0 0 -1
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0 0 -1 0
119 120 1.0
119 121 1.0
122 123 1.0 1 0 0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Production, cumulative 300 ps¶
Provenance: /home/ubuntu/work/03-production_workdir/prod_0300ps
LoadSystem
File /home/ubuntu/work/03-production_workdir/prod_0250ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 600000
Restart /home/ubuntu/work/03-production_workdir/prod_0250ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 7.8476114248 3.2440313037 7.2146945844 region=glycine
C 8.5184080911 2.3879859765 8.2427186872 region=glycine
C 10.0080210162 2.0845541718 7.8849513465 region=glycine
O 10.5440643611 1.1817620180 8.4481533910 region=glycine
O 10.6670321163 2.8608571071 6.9533301758 region=glycine
H 7.5093715702 2.8421891859 6.3131255204 region=glycine
H 8.0988939179 4.1621019964 7.1786556754 region=glycine
H 7.9668183454 1.4571952417 8.2929554315 region=glycine
H 8.4091746536 2.8550661357 9.2392957844 region=glycine
H 9.9222915781 3.4814207610 6.7075470909 region=glycine
O 9.3362117422 7.5221735152 4.6315425795 region=water
H 9.7262660621 8.0817370974 5.2686058278 region=water
H 9.4453339328 7.9750854449 3.7981662326 region=water
O 4.2806646132 7.5190077509 9.4447405967 region=water
H 3.9140664756 6.7594793559 10.0357324061 region=water
H 3.5279078525 8.2049887725 9.3491546836 region=water
O 6.9024650935 5.2359878287 4.1223086332 region=water
H 7.7584588171 5.0760341303 3.8064612408 region=water
H 6.4149354945 4.5117607505 3.7343634149 region=water
O 8.9502910498 3.5232338449 10.7856977118 region=water
H 8.6835205864 4.4506595120 10.9377044041 region=water
H 9.9617169894 3.6322733929 10.7240191364 region=water
O 9.3491567208 5.4653035269 6.6960456725 region=water
H 9.5004368159 6.0054581260 5.9081088931 region=water
H 8.8032357018 5.9656343717 7.2762930177 region=water
O 7.7397169240 5.9819991470 0.6155817308 region=water
H 8.5707154068 6.4819921036 0.5928476008 region=water
H 7.3752933263 6.2102480873 10.6483638673 region=water
O 4.1822910982 9.5373399962 2.6617967704 region=water
H 4.5856364098 10.0535776025 1.8686934143 region=water
H 3.7550987575 8.7672344867 2.1849365318 region=water
O 6.4098014124 9.6216429835 4.4374921376 region=water
H 6.3679434503 8.8284798168 5.0861031219 region=water
H 6.0477337301 9.3501728470 3.5802531073 region=water
O 1.7456931982 9.9857312823 0.0214005511 region=water
H 2.4971595301 10.6651526360 0.1510087436 region=water
H 1.7930118835 9.7974084980 10.0893901572 region=water
O 1.6735847718 4.6163586138 8.9313715323 region=water
H 1.7089889058 3.6593187388 8.8207265456 region=water
H 2.3940307239 4.8629276989 9.5162992792 region=water
O 4.6828040152 0.3347401056 0.3325352165 region=water
H 4.7678101743 1.1181212461 0.9479629767 region=water
H 5.3428705372 0.6343612703 10.6666285861 region=water
O 0.1469046427 8.7528453414 6.5089086640 region=water
H 0.7875968102 9.1486109325 5.8806306815 region=water
H 0.5815869747 8.2204394644 7.1395508029 region=water
O 5.4020728600 2.5786639596 9.9341179326 region=water
H 4.4275415854 2.6562583726 10.1084407730 region=water
H 5.6662368730 3.3998781441 9.4054284962 region=water
O 3.9288791295 2.8885881334 5.4807833599 region=water
H 4.3383886297 2.0565038428 5.6676801746 region=water
H 4.6348312751 3.3169180749 4.8896741342 region=water
O 2.4696676456 10.3377318077 8.1714495584 region=water
H 2.9992648038 0.1036161538 8.4817148352 region=water
H 1.5531831937 10.6609992863 8.2314744665 region=water
O 9.0183002453 10.3547735353 10.3009790248 region=water
H 8.6176836578 9.8117731122 9.6004994378 region=water
H 9.4439727330 0.1197264994 9.7813190655 region=water
O 1.0064920988 1.3262024734 4.5787331894 region=water
H 1.1410785103 2.0732105413 3.9467569583 region=water
H 0.6644313856 1.7193931781 5.3823860989 region=water
O 5.5719346730 0.0815080445 8.4582000390 region=water
H 5.1208493412 0.1865007877 7.6146927008 region=water
H 5.3526050015 0.7556892193 9.0443462824 region=water
O 4.8931503898 3.9328953112 2.8142435746 region=water
H 4.6192632984 2.9826135529 2.6571147840 region=water
H 4.0116519869 4.3106941129 3.0792833932 region=water
O 1.8344175949 7.9153024954 2.0384724052 region=water
H 2.0276120496 8.4705107496 2.7916474028 region=water
H 1.6731276331 8.6468075616 1.3143034957 region=water
O 1.2658877493 7.4810276386 8.5783242421 region=water
H 1.5611057223 6.6688400008 8.2175496614 region=water
H 0.6698900296 7.3146325829 9.2790836204 region=water
O 0.9473786358 1.9848170021 0.9425378461 region=water
H 0.5067131076 2.8226377643 0.8502131586 region=water
H 1.7405476708 2.1238214521 1.4919843672 region=water
O 9.1993861662 3.7777100574 3.0332484539 region=water
H 9.1987024735 2.8410887167 3.3419727270 region=water
H 8.9982406268 3.8422334082 2.0546343574 region=water
O 9.3452661509 0.9986305417 3.7538974569 region=water
H 9.0483915983 0.2466074162 3.3250659542 region=water
H 10.2848535212 0.9522068035 3.6621557432 region=water
O 0.1980050140 4.6198124224 0.3136051326 region=water
H 10.7507894643 5.4615040625 0.5489358305 region=water
H 0.8138051533 4.7865195322 10.5694638879 region=water
O 6.9026538560 6.9463491236 9.2470577727 region=water
H 6.5932094267 6.2281528159 8.6604668301 region=water
H 5.9699975608 7.2703479105 9.4605146194 region=water
O 5.7629745590 4.5574756540 8.1613002192 region=water
H 4.8687607039 4.8676080269 7.6661810167 region=water
H 6.2059297448 3.8720345248 7.6611020035 region=water
O 7.1868863929 1.7905708584 1.0661608716 region=water
H 8.0677954423 2.1168660073 0.9787165950 region=water
H 6.7278659168 1.9932129152 0.2520568094 region=water
O 8.7995936192 9.2056909444 2.4303294753 region=water
H 7.9288033152 8.9382506268 2.5975289690 region=water
H 8.6360557471 9.7940583671 1.7555018042 region=water
O 5.5508296781 7.3197547068 5.7273867728 region=water
H 4.8829998665 6.9185643898 6.3052398928 region=water
H 6.0472293189 6.5108641440 5.3767088257 region=water
O 6.6546154937 1.6791851536 5.0412701724 region=water
H 5.9669115789 0.9973846269 5.3249740390 region=water
H 7.4375590679 1.2072395704 4.6980950889 region=water
O 3.3681434528 1.4167749523 2.8506571966 region=water
H 2.6283466109 1.0051643057 3.3165380618 region=water
H 4.0554357327 0.7306334684 3.1407842427 region=water
O 2.9766092267 1.7441668329 9.9156670649 region=water
H 3.2176056865 1.1690707589 10.7049004013 region=water
H 2.2110887309 2.2012847947 10.2293772842 region=water
O 3.4676232511 5.4088110260 6.7573824782 region=water
H 3.3709427999 4.5630194905 6.2609721025 region=water
H 2.7049479602 5.4446306021 7.3501063193 region=water
O 1.8878833881 9.8680863394 4.4983684270 region=water
H 1.8964216331 10.8188157527 4.6969502462 region=water
H 2.7762651904 9.7085710177 3.9645680744 region=water
O 4.2017141971 0.1002110267 5.9509568556 region=water
H 3.4645196217 10.5898786303 6.3591149113 region=water
H 4.7359569552 10.3097304303 5.7089181907 region=water
O 10.2012586102 7.3841199130 0.7166147136 region=water
H 9.5570312984 7.9561965879 1.0951402333 region=water
H 0.0782528964 7.7178849319 1.0503187973 region=water
O 3.9552958978 5.1748646937 0.0361931584 region=water
H 3.8024220352 4.9621288684 0.9658842701 region=water
H 4.3656814459 4.4012600720 10.6822694081 region=water
O 6.5513371423 7.3478765613 2.5643859420 region=water
H 6.9881005153 6.8515999915 1.8283537075 region=water
H 6.5246279360 6.5981590733 3.2599735333 region=water
O 2.6150296506 5.5319560812 2.7634730943 region=water
H 2.6062230590 6.2440247894 2.2050507943 region=water
H 1.6046140173 5.3916484312 2.9936969646 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0 0 0 -1
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0 0 0 -1
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0 0 0 -1
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0 0 1 0
53 55 1.0
56 57 1.0
56 58 1.0 0 1 0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0 -1 0 0
83 85 1.0 0 0 -1
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0 0 -1 0
116 118 1.0 0 -1 0
119 120 1.0
119 121 1.0 1 0 0
122 123 1.0
122 124 1.0 0 0 -1
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
Final MSD analysis¶
Provenance: /home/ubuntu/work/03-production_workdir/msd_0300ps
MeanSquareDisplacement
Atoms
Region glycine
end
ComputeStandardDeviation Yes
MaxFrame 200
Property DiffusionCoefficient
StartTimeSlope 5000.0
UseMolecularCentersOfMass
CheckForBondChanges Yes
Enabled Yes
end
end
Task MeanSquareDisplacement
TrajectoryInfo
Trajectory
KFFilename /home/ubuntu/work/03-production_workdir/prod_0300ps/ams.rkf
end
end
Conclusion¶
The final glycine center-of-mass diffusion coefficient is 1.511364e-09 m^2/s with a fitted MSD R^2 of 0.997441. The last three cumulative estimates are each within 15% of their mean, so the production estimate is converged by the specified test.
Prompts and Python scripts¶
Prompt (instruction for AI agent)
Use the ams2026 skill!
# Glycine diffusion with ReaxFF at 380 K
## Summary
Build a periodic cubic system containing one neutral glycine molecule
(non-zwitterionic) and 40 water molecules at 1.0 g/cm3.
Use ReaxFF Glycine.ff for iterative NVT equilibration, followed by a separate
NVT production trajectory initialized from the final equilibrated coordinates
and velocities. Report the glycine center-of-mass diffusion coefficient from
its MSD.
Run all ReaxFF simulations with nproc=1 to disable MPI (it will automatically
use OpenMP).
## Implementation
Be verbose with `plams.log("message")` lines, especially when testing
equilibration and production convergence (criteria vs measured values,
failure/success, ...).
Make the equilibration and production scripts restartable from themselves, in
case there are errors in the scripts, so that any completed MD simulations can
be reused.
### Script 1: initial system
- Pack the molecules, retain explicit glycine and water regions, remove bad
contacts with a ReaxFF geometry optimization (Convergence.Quality basic).
### Script 2: equilibration
- Timestep 0.5 fs, sample every 100 fs
- Equilibrate at 380 K with a Berendsen thermostat and 100 fs coupling time.
Extend in 5 ps increments with Restart and CopyRestartTrajectory Yes, up to
100 ps.
- After at least 10 ps, examine the trailing half of the accumulated
trajectory. Divide it into five blocks and fit block-mean potential energy
against time. Accept equilibration after two consecutive checks where the
fitted change across the window is at most 0.5 trajectory standard
deviations. Also require the mean temperature to be within 2% of 380 K.
### Script 3: production
- Timestep 0.5 fs, sample every 100 fs
- Start a production NVT job from the final equilibrated structure and
velocities without copying equilibration frames. Use an NHC thermostat with
100 fs coupling.
- Run at least 100 ps of production, then extend in 50 ps increments using
CopyRestartTrajectory, with a 1 ns cap.
- Use the `UseMolecularCentersOfMass` input block/option to trajectory analysis
to get center-of-mass diffusion.
- Calculate the MSD in a 20 ps window starting the fit at 5 ps.
- Declare convergence when the last three cumulative diffusion estimates each
lie within 15% of their mean. If the 1 ns cap is reached, report the best
estimate as unconverged.
- The MSD calculation center-of-mass fails on glycine fragmentation or atom
exchange. If this happens, do not equilibrate further but report the final
results and the fragmentation status.
The production simulation may take a long time to finish. Once everything seems
to be working correctly, you can monitor/poll the simulation less frequently.
### Reporting script
- Produce tables of convergence history, potential-energy and temperature
traces, MSD and fitted-region figures, and an image of the packed system.
- Include the final diffusion coefficient in m2/s (exponential notation), the
fit interval, trajectory length, convergence status, observed temperature and
pressure, and the complete AMS inputs.
- Note the finite-size limitation from using only 40 water molecules and the
fixed-density NVT state.
## Assumptions
- “Diffusion coefficient” means translational diffusion of the glycine
molecular center of mass.
- The initial glycine form is neutral NH2-CH2-COOH.
- No finite-size correction or independent replicate trajectories are
requested.
01-initial-system.py
#!/usr/bin/env amspython
from __future__ import annotations
from scm.plams import AMSJob, Settings, finish, from_smiles, init, log, packmol
from common import completed_jobs, reaxff_settings
def main() -> None:
reusable = completed_jobs("01-initial-system_workdir", "setup_opt")
if reusable:
job = reusable["setup_opt"]
log(f"Reusing completed ReaxFF geometry optimization at {job.path}.")
return
log("Building neutral glycine NH2-CH2-COOH from SMILES NCC(=O)O.")
glycine = from_smiles("NCC(=O)O")
water = from_smiles("O")
log(f"Glycine has {len(glycine)} atoms and formal charge {glycine.properties.get('charge', 0)}.")
log("Packing one glycine and 40 water molecules at an overall density of 1.0 g/cm^3.")
packed = packmol(
molecules=[glycine, water],
n_molecules=[1, 40],
density=1.0,
region_names=["glycine", "water"],
keep_bonds=True,
seed=38040,
)
log(f"Packed system has {len(packed)} atoms, regions glycine and water, "
f"and density {packed.get_density() / 1000:.6f} g/cm^3.")
settings = reaxff_settings()
settings.input.ams.Task = "GeometryOptimization"
settings.input.ams.GeometryOptimization.Convergence.Quality = "Basic"
job = AMSJob(name="setup_opt", molecule=packed, settings=settings)
log("Starting ReaxFF bad-contact removal with GeometryOptimization Convergence Quality Basic.")
job.run()
if not job.ok():
raise RuntimeError(f"Initial ReaxFF geometry optimization failed: {job.results.get_errormsg()}")
log(f"Initial ReaxFF geometry optimization succeeded at {job.path}.")
if __name__ == "__main__":
init(folder="01-initial-system_workdir")
try:
main()
finally:
finish()
02-equilibration.py
#!/usr/bin/env amspython
from __future__ import annotations
from scm.plams import AMSJob, AMSNVTJob, finish, init, log
from common import (
SAMPLING_FREQUENCY,
TARGET_TEMPERATURE_K,
TIMESTEP_FS,
completed_jobs,
equilibration_metrics,
log_equilibration_check,
restart_settings,
reaxff_settings,
sorted_cumulative_jobs,
)
INCREMENT_PS = 5
MAXIMUM_PS = 100
STEPS_PER_INCREMENT = int(INCREMENT_PS * 1000 / TIMESTEP_FS)
def run_first_segment(setup_job: AMSJob) -> AMSJob:
job = AMSNVTJob(
name="eq_005ps",
molecule=setup_job.results.get_main_molecule(),
settings=reaxff_settings(),
nsteps=STEPS_PER_INCREMENT,
timestep=TIMESTEP_FS,
samplingfreq=SAMPLING_FREQUENCY,
temperature=TARGET_TEMPERATURE_K,
thermostat="Berendsen",
tau=100.0,
calcpressure=True,
writevelocities=True,
writebonds=True,
writemolecules=True,
)
log("Starting the first 5 ps Berendsen NVT equilibration segment from optimized coordinates.")
job.run()
if not job.ok():
raise RuntimeError(f"Equilibration segment failed: {job.results.get_errormsg()}")
log(f"Completed the cumulative 5 ps equilibration trajectory at {job.path}.")
return job
def extend(previous_job: AMSJob, target_ps: int) -> AMSJob:
target_steps = int(target_ps * 1000 / TIMESTEP_FS)
settings = restart_settings(previous_job, target_steps)
job = AMSJob(name=f"eq_{target_ps:03d}ps", molecule=None, settings=settings)
log(f"Extending equilibration exactly from {previous_job.name} to {target_ps} ps with Restart and "
"CopyRestartTrajectory Yes.")
job.run()
if not job.ok():
raise RuntimeError(f"Equilibration extension to {target_ps} ps failed: {job.results.get_errormsg()}")
log(f"Completed the cumulative {target_ps} ps equilibration trajectory at {job.path}.")
return job
def main() -> None:
setup_jobs = completed_jobs("01-initial-system_workdir", "setup_opt")
if not setup_jobs:
raise RuntimeError("No completed setup_opt job. Run 01-initial-system.py first.")
setup_job = setup_jobs["setup_opt"]
known = completed_jobs("02-equilibration_workdir", "eq_*ps")
cumulative = sorted_cumulative_jobs(known, "eq_")
if cumulative:
log(f"Found {len(cumulative)} reusable completed equilibration trajectories; latest is "
f"{cumulative[-1][0]} ps at {cumulative[-1][1].path}.")
else:
first = run_first_segment(setup_job)
cumulative = [(INCREMENT_PS, first)]
streak = 0
converged = False
for duration_ps, job in cumulative:
if duration_ps < 10:
log(f"Skipping the equilibration convergence test at {duration_ps} ps; at least 10 ps is required.")
continue
metrics = equilibration_metrics(job)
streak = streak + 1 if metrics["passed"] else 0
log_equilibration_check(duration_ps, metrics, streak)
if streak >= 2:
converged = True
log(f"Equilibration accepted at {duration_ps} ps after two consecutive passing checks.")
break
while not converged and cumulative[-1][0] < MAXIMUM_PS:
target_ps = cumulative[-1][0] + INCREMENT_PS
job = extend(cumulative[-1][1], target_ps)
cumulative.append((target_ps, job))
if target_ps < 10:
continue
metrics = equilibration_metrics(job)
streak = streak + 1 if metrics["passed"] else 0
log_equilibration_check(target_ps, metrics, streak)
if streak >= 2:
converged = True
log(f"Equilibration accepted at {target_ps} ps after two consecutive passing checks.")
if not converged:
log("Equilibration reached the 100 ps cap without two consecutive passing checks. "
"The final capped trajectory will be used for production and reported as not equilibrated by the test.")
if __name__ == "__main__":
init(folder="02-equilibration_workdir")
try:
main()
finally:
finish()
03-production.py
#!/usr/bin/env amspython
from __future__ import annotations
from pathlib import Path
from typing import Dict, Optional
import numpy as np
from scm.plams import AMSJob, AMSMSDJob, AMSNVTJob, Settings, finish, init, log
from common import (
SAMPLING_FREQUENCY,
TARGET_TEMPERATURE_K,
TIMESTEP_FS,
completed_jobs,
fragmentation_failure_paths,
restart_settings,
sorted_cumulative_jobs,
)
INITIAL_PS = 100
INCREMENT_PS = 50
MAXIMUM_PS = 1000
MSD_WINDOW_FS = 20_000.0
MSD_FIT_START_FS = 5_000.0
def start_production(equilibration_job: AMSJob) -> AMSJob:
overrides = Settings()
job = AMSNVTJob.restart_from(
equilibration_job,
name="prod_100ps",
settings=overrides,
nsteps=int(INITIAL_PS * 1000 / TIMESTEP_FS),
timestep=TIMESTEP_FS,
samplingfreq=SAMPLING_FREQUENCY,
temperature=TARGET_TEMPERATURE_K,
thermostat="NHC",
tau=100.0,
calcpressure=True,
writevelocities=True,
writebonds=True,
writemolecules=True,
)
md = job.settings.input.ams.MolecularDynamics
if "Restart" in md:
del md.Restart
if "CopyRestartTrajectory" in md:
del md.CopyRestartTrajectory
if "LoadSystem" in job.settings.input.ams:
del job.settings.input.ams.LoadSystem
log("Starting a separate 100 ps production NVT trajectory with an NHC thermostat. "
"Only the final equilibration coordinates and velocities are loaded; equilibration frames are not copied.")
job.run()
if not job.ok():
raise RuntimeError(f"Initial production trajectory failed: {job.results.get_errormsg()}")
log(f"Completed the cumulative 100 ps production trajectory at {job.path}.")
return job
def extend(previous_job: AMSJob, target_ps: int) -> AMSJob:
settings = restart_settings(previous_job, int(target_ps * 1000 / TIMESTEP_FS))
job = AMSJob(name=f"prod_{target_ps:04d}ps", molecule=None, settings=settings)
log(f"Extending production exactly from {previous_job.name} to {target_ps} ps with Restart and "
"CopyRestartTrajectory Yes.")
job.run()
if not job.ok():
raise RuntimeError(f"Production extension to {target_ps} ps failed: {job.results.get_errormsg()}")
log(f"Completed the cumulative {target_ps} ps production trajectory at {job.path}.")
return job
def analysis_settings() -> Settings:
settings = Settings()
msd = settings.input.MeanSquareDisplacement
msd.Atoms.Region = "glycine"
msd.UseMolecularCentersOfMass.Enabled = "Yes"
msd.UseMolecularCentersOfMass.CheckForBondChanges = "Yes"
msd.ComputeStandardDeviation = "Yes"
return settings
def reusable_msd_job(name: str) -> Optional[AMSMSDJob]:
candidates = []
from common import ROOT, natural_key
for workdir in ROOT.glob("03-production_workdir*"):
path = workdir / name
if path.is_dir() and (path / f"{name}.err").is_file():
candidates.append(path)
for path in sorted(candidates, key=lambda item: natural_key(str(item))):
try:
job = AMSMSDJob.load_external(str(path))
if job.ok():
return job
except Exception as exc:
log(f"Could not reuse MSD analysis at {path}: {exc}")
return None
def run_msd(production_job: AMSJob, duration_ps: int) -> Optional[float]:
name = f"msd_{duration_ps:04d}ps"
job = reusable_msd_job(name)
if job is not None:
value = float(job.results.get_diffusion_coefficient(
start_time_fit_fs=MSD_FIT_START_FS, end_time_fit_fs=MSD_WINDOW_FS
))
log(f"Reusing {name}: D = {value:.6e} m^2/s from the 5-20 ps fit interval.")
return value
log(f"Running glycine molecular-center-of-mass MSD analysis for the cumulative {duration_ps} ps trajectory. "
"The correlation window is 20 ps and the linear fit interval is 5-20 ps.")
job = AMSMSDJob(
previous_job=production_job,
name=name,
max_correlation_time_fs=MSD_WINDOW_FS,
start_time_fit_fs=MSD_FIT_START_FS,
settings=analysis_settings(),
)
try:
job.run()
if not job.ok():
text = " ".join(job.results.grep_output("bond", options="-i") or [])
if "bond" in text.lower():
log("Molecular-center-of-mass MSD failed because the glycine bonding changed. "
"Production will stop and the fragmentation status will be reported.")
return None
raise RuntimeError(f"MSD analysis failed: {job.results.get_errormsg()}")
value = float(job.results.get_diffusion_coefficient(
start_time_fit_fs=MSD_FIT_START_FS, end_time_fit_fs=MSD_WINDOW_FS
))
except Exception as exc:
text = str(exc).lower()
job_text = ""
if job.path:
from common import read_job_text
job_text = read_job_text(Path(job.path)).lower()
combined = text + "\n" + job_text
if "bond" in combined and any(word in combined for word in ("change", "changed", "molecule", "fragment")):
log(f"Molecular-center-of-mass MSD detected glycine fragmentation or atom exchange: {exc}")
return None
raise
log(f"Cumulative {duration_ps} ps diffusion estimate: D = {value:.6e} m^2/s.")
return value
def converged(estimates: Dict[int, float]) -> bool:
if len(estimates) < 3:
log(f"Production convergence needs three cumulative estimates; only {len(estimates)} are available.")
return False
durations = sorted(estimates)[-3:]
values = np.asarray([estimates[duration] for duration in durations], dtype=float)
mean = float(values.mean())
relative = np.abs(values - mean) / abs(mean) if mean != 0.0 else np.full(3, np.inf)
for duration, value, deviation in zip(durations, values, relative):
log(f"Production convergence member at {duration} ps: D = {value:.6e} m^2/s; "
f"deviation from three-estimate mean = {100 * deviation:.3f}%; required <= 15.000%.")
passed = bool(np.all(relative <= 0.15))
log(f"Production convergence check using {durations}: mean D = {mean:.6e} m^2/s; "
f"{'PASS' if passed else 'FAIL'}.")
return passed
def main() -> None:
prior_fragmentation = fragmentation_failure_paths()
if prior_fragmentation:
log(f"A prior center-of-mass analysis recorded bond changes at {prior_fragmentation[-1]}. "
"No further production MD will be run.")
return
equilibration = sorted_cumulative_jobs(completed_jobs("02-equilibration_workdir", "eq_*ps"), "eq_")
if not equilibration:
raise RuntimeError("No completed equilibration job. Run 02-equilibration.py first.")
final_equilibration = equilibration[-1][1]
log(f"Using the final cumulative equilibration trajectory {final_equilibration.name} at "
f"{final_equilibration.path} to initialize production.")
cumulative = sorted_cumulative_jobs(completed_jobs("03-production_workdir", "prod_*ps"), "prod_")
if cumulative:
log(f"Found {len(cumulative)} reusable completed production trajectories; latest is "
f"{cumulative[-1][0]} ps at {cumulative[-1][1].path}.")
else:
first = start_production(final_equilibration)
cumulative = [(INITIAL_PS, first)]
estimates: Dict[int, float] = {}
for duration_ps, job in cumulative:
value = run_msd(job, duration_ps)
if value is None:
return
estimates[duration_ps] = value
if converged(estimates):
log(f"Production already converged at {max(estimates)} ps; no extension is needed.")
return
while cumulative[-1][0] < MAXIMUM_PS:
target_ps = min(cumulative[-1][0] + INCREMENT_PS, MAXIMUM_PS)
job = extend(cumulative[-1][1], target_ps)
cumulative.append((target_ps, job))
value = run_msd(job, target_ps)
if value is None:
return
estimates[target_ps] = value
if converged(estimates):
log(f"Production diffusion estimate converged at {target_ps} ps.")
return
log(f"Production reached the 1 ns cap without convergence. The latest estimate, "
f"D = {estimates[MAXIMUM_PS]:.6e} m^2/s, will be reported as unconverged.")
if __name__ == "__main__":
init(folder="03-production_workdir")
try:
main()
finally:
finish()
common.py
from __future__ import annotations
import re
from pathlib import Path
from typing import Dict, List, Optional, Tuple
import numpy as np
from scm.plams import AMSJob, Settings, log
ROOT = Path(__file__).resolve().parent
FORCE_FIELD = "Glycine.ff"
TIMESTEP_FS = 0.5
SAMPLING_INTERVAL_FS = 100.0
SAMPLING_FREQUENCY = int(SAMPLING_INTERVAL_FS / TIMESTEP_FS)
TARGET_TEMPERATURE_K = 380.0
def natural_key(value: str) -> List[object]:
return [int(part) if part.isdigit() else part.lower() for part in re.split(r"(\d+)", value)]
def job_paths(workdir_prefix: str, name_pattern: str) -> List[Path]:
paths: List[Path] = []
for workdir in ROOT.glob(f"{workdir_prefix}*"):
if not workdir.is_dir():
continue
for path in workdir.glob(name_pattern):
if path.is_dir() and (path / "ams.rkf").is_file():
paths.append(path)
return sorted(paths, key=lambda path: natural_key(str(path)))
def load_completed(path: Path) -> Optional[AMSJob]:
try:
job = AMSJob.load_external(str(path))
if job.ok():
return job
except Exception as exc:
log(f"Could not reuse {path}: {exc}")
return None
def completed_jobs(workdir_prefix: str, name_pattern: str) -> Dict[str, AMSJob]:
found: Dict[str, AMSJob] = {}
for path in job_paths(workdir_prefix, name_pattern):
job = load_completed(path)
if job is not None:
found[path.name] = job
return found
def reaxff_settings() -> Settings:
settings = Settings()
settings.input.ReaxFF.ForceField = FORCE_FIELD
settings.runscript.nproc = 1
return settings
def duration_from_name(name: str) -> int:
match = re.search(r"_(\d+)ps$", name)
if match is None:
raise ValueError(f"Cannot read trajectory duration from job name {name!r}")
return int(match.group(1))
def sorted_cumulative_jobs(jobs: Dict[str, AMSJob], prefix: str) -> List[Tuple[int, AMSJob]]:
items = [(duration_from_name(name), job) for name, job in jobs.items() if name.startswith(prefix)]
return sorted(items, key=lambda item: item[0])
def equilibration_metrics(job: AMSJob) -> Dict[str, float | bool]:
times = np.asarray(job.results.get_history_property("Time", "MDHistory"), dtype=float)
energies = np.asarray(job.results.get_history_property("PotentialEnergy", "MDHistory"), dtype=float)
temperatures = np.asarray(job.results.get_history_property("Temperature", "MDHistory"), dtype=float)
start = float(times.min() + 0.5 * (times.max() - times.min()))
mask = times >= start
trailing_times = times[mask]
trailing_energies = energies[mask]
trailing_temperatures = temperatures[mask]
if len(trailing_times) < 10:
raise RuntimeError("Too few trajectory samples for the five-block equilibration test")
blocks = np.array_split(np.arange(len(trailing_times)), 5)
block_times = np.asarray([trailing_times[block].mean() for block in blocks])
block_energies = np.asarray([trailing_energies[block].mean() for block in blocks])
slope, _ = np.polyfit(block_times, block_energies, 1)
fitted_change = float(slope * (block_times[-1] - block_times[0]))
trajectory_std = float(np.std(trailing_energies, ddof=1))
energy_ratio = abs(fitted_change) / trajectory_std if trajectory_std > 0.0 else float("inf")
mean_temperature = float(np.mean(trailing_temperatures))
temperature_relative_error = abs(mean_temperature - TARGET_TEMPERATURE_K) / TARGET_TEMPERATURE_K
energy_ok = bool(energy_ratio <= 0.5)
temperature_ok = bool(temperature_relative_error <= 0.02)
return {
"window_start_fs": start,
"window_end_fs": float(times.max()),
"fitted_change_hartree": fitted_change,
"trajectory_std_hartree": trajectory_std,
"energy_change_in_std": energy_ratio,
"mean_temperature_k": mean_temperature,
"temperature_relative_error": temperature_relative_error,
"energy_ok": energy_ok,
"temperature_ok": temperature_ok,
"passed": bool(energy_ok and temperature_ok),
}
def log_equilibration_check(duration_ps: int, metrics: Dict[str, float | bool], streak: int) -> None:
log(f"Equilibration check at {duration_ps} ps uses the trailing window "
f"{float(metrics['window_start_fs']) / 1000:.3f}-{float(metrics['window_end_fs']) / 1000:.3f} ps.")
log(f"Potential-energy criterion: |fitted change| / trajectory standard deviation = "
f"{float(metrics['energy_change_in_std']):.4f}; required <= 0.5000; "
f"{'PASS' if metrics['energy_ok'] else 'FAIL'}.")
log(f"Temperature criterion: trailing mean = {float(metrics['mean_temperature_k']):.3f} K; "
f"relative error = {100 * float(metrics['temperature_relative_error']):.3f}%; required <= 2.000%; "
f"{'PASS' if metrics['temperature_ok'] else 'FAIL'}.")
log(f"Combined equilibration check: {'PASS' if metrics['passed'] else 'FAIL'}; "
f"consecutive passing checks = {streak}; required = 2.")
def restart_settings(previous_job: AMSJob, target_steps: int) -> Settings:
settings = previous_job.settings.copy()
md = settings.input.ams.MolecularDynamics
if "InitialVelocities" in md:
del md.InitialVelocities
md.NSteps = target_steps
md.Restart = previous_job.results.rkfpath()
md.CopyRestartTrajectory = "Yes"
settings.input.ams.LoadSystem = [
Settings(_h="", file=previous_job.results.rkfpath(), section="Molecule")
]
return settings
def read_job_text(path: Path) -> str:
chunks: List[str] = []
for suffix in ("*.err", "*.out", "*.log"):
for file_path in path.glob(suffix):
try:
chunks.append(file_path.read_text(errors="replace"))
except OSError:
pass
return "\n".join(chunks)
def fragmentation_failure_paths() -> List[Path]:
from scm.plams import AMSMSDJob
failures: List[Path] = []
for workdir in ROOT.glob("03-production_workdir*"):
for path in workdir.glob("msd_*ps"):
if not path.is_dir():
continue
try:
if AMSMSDJob.load_external(str(path)).ok():
continue
except Exception:
pass
text = read_job_text(path).lower()
if "bond" in text and any(word in text for word in ("change", "changed", "molecule", "fragment")):
failures.append(path)
return sorted(failures, key=lambda path: natural_key(str(path)))
report.py
#!/usr/bin/env amspython
from __future__ import annotations
from pathlib import Path
from typing import Dict, List, Optional, Tuple
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scm.base import Units
from scm.plams import AMSJob, AMSMSDJob, log, view
from common import (
ROOT,
TARGET_TEMPERATURE_K,
completed_jobs,
equilibration_metrics,
fragmentation_failure_paths,
natural_key,
sorted_cumulative_jobs,
)
TABLES = ROOT / "tables"
FIGURES = ROOT / "figures"
MSD_FIT_START_FS = 5_000.0
MSD_WINDOW_FS = 20_000.0
def successful_msd_jobs() -> Dict[int, AMSMSDJob]:
found: Dict[int, AMSMSDJob] = {}
candidates: List[Path] = []
for workdir in ROOT.glob("03-production_workdir*"):
candidates.extend(path for path in workdir.glob("msd_*ps") if path.is_dir())
for path in sorted(candidates, key=lambda item: natural_key(str(item))):
try:
job = AMSMSDJob.load_external(str(path))
if job.ok():
duration = int(path.name.split("_")[1][:-2])
found[duration] = job
except Exception as exc:
log(f"Skipping unreadable MSD analysis at {path}: {exc}")
return found
def equilibration_table(equilibration: List[Tuple[int, AMSJob]]) -> pd.DataFrame:
rows: List[dict] = []
streak = 0
for duration, job in equilibration:
if duration < 10:
continue
metrics = equilibration_metrics(job)
streak = streak + 1 if metrics["passed"] else 0
rows.append({
"duration_ps": duration,
"window_start_ps": float(metrics["window_start_fs"]) / 1000,
"window_end_ps": float(metrics["window_end_fs"]) / 1000,
"fitted_energy_change_hartree": metrics["fitted_change_hartree"],
"energy_std_hartree": metrics["trajectory_std_hartree"],
"abs_change_over_std": metrics["energy_change_in_std"],
"mean_temperature_k": metrics["mean_temperature_k"],
"temperature_error_percent": 100 * float(metrics["temperature_relative_error"]),
"energy_pass": metrics["energy_ok"],
"temperature_pass": metrics["temperature_ok"],
"combined_pass": metrics["passed"],
"consecutive_passes": streak,
"accepted": streak >= 2,
})
return pd.DataFrame(rows)
def production_table(msd_jobs: Dict[int, AMSMSDJob]) -> pd.DataFrame:
rows: List[dict] = []
estimates: Dict[int, float] = {}
for duration in sorted(msd_jobs):
value = float(msd_jobs[duration].results.get_diffusion_coefficient(
start_time_fit_fs=MSD_FIT_START_FS, end_time_fit_fs=MSD_WINDOW_FS
))
estimates[duration] = value
last = sorted(estimates)[-3:]
mean: Optional[float] = None
maximum_deviation: Optional[float] = None
converged = False
if len(last) == 3:
values = np.asarray([estimates[item] for item in last])
mean = float(values.mean())
deviations = np.abs(values - mean) / abs(mean) if mean != 0.0 else np.full(3, np.inf)
maximum_deviation = float(deviations.max())
converged = bool(np.all(deviations <= 0.15))
rows.append({
"duration_ps": duration,
"diffusion_m2_s": value,
"last_three_mean_m2_s": mean,
"last_three_max_deviation_percent": None if maximum_deviation is None else 100 * maximum_deviation,
"converged": converged,
})
return pd.DataFrame(rows)
def history_frame(job: AMSJob, stage: str) -> pd.DataFrame:
time = np.asarray(job.results.get_history_property("Time", "MDHistory"), dtype=float)
energy = np.asarray(job.results.get_history_property("PotentialEnergy", "MDHistory"), dtype=float)
temperature = np.asarray(job.results.get_history_property("Temperature", "MDHistory"), dtype=float)
pressure_au = np.asarray(job.results.get_history_property("Pressure", "MDHistory"), dtype=float)
energy_factor = Units.conversion_factor("hartree", "kJ/mol")
pressure_factor = Units.conversion_factor("au", "Pa")
return pd.DataFrame({
"stage": stage,
"time_fs": time,
"potential_energy_hartree": energy,
"potential_energy_kj_mol": energy * energy_factor,
"temperature_k": temperature,
"pressure_pa": pressure_au * pressure_factor,
})
def make_trace_figure(eq_trace: pd.DataFrame, prod_trace: pd.DataFrame) -> None:
fig, axes = plt.subplots(2, 1, figsize=(8, 7), sharex=False)
for frame, label in ((eq_trace, "Equilibration"), (prod_trace, "Production")):
axes[0].plot(frame["time_fs"] / 1000, frame["potential_energy_kj_mol"], label=label)
axes[1].plot(frame["time_fs"] / 1000, frame["temperature_k"], label=label)
axes[0].set_ylabel("Potential energy (kJ/mol)")
axes[1].set_ylabel("Temperature (K)")
axes[1].set_xlabel("Trajectory time (ps)")
axes[1].axhline(TARGET_TEMPERATURE_K, color="black", linewidth=0.8, linestyle=":")
for axis in axes:
axis.legend()
axis.grid(alpha=0.2)
fig.tight_layout()
fig.savefig(FIGURES / "potential-energy-temperature.png", dpi=180)
plt.close(fig)
def make_msd_figure(job: AMSMSDJob) -> pd.DataFrame:
time, msd = job.results.get_msd()
fit, fit_time, fit_msd = job.results.get_linear_fit(
start_time_fit_fs=MSD_FIT_START_FS, end_time_fit_fs=MSD_WINDOW_FS
)
frame = pd.DataFrame({"time_fs": time, "msd_angstrom2": msd})
frame.to_csv(TABLES / "glycine-com-msd.csv", index=False)
fig, ax = plt.subplots(figsize=(7, 4.5))
ax.plot(time / 1000, msd, label="Glycine COM MSD")
ax.plot(fit_time / 1000, fit_msd, label="Linear fit, 5-20 ps")
ax.axvspan(5, 20, color="tab:orange", alpha=0.12)
ax.set_xlabel("Correlation time (ps)")
ax.set_ylabel("MSD (angstrom^2)")
ax.grid(alpha=0.2)
ax.legend()
fig.tight_layout()
fig.savefig(FIGURES / "glycine-com-msd-fit.png", dpi=180)
plt.close(fig)
return frame
def input_section(title: str, job: AMSJob) -> str:
return f"### {title}\n\nProvenance: `{job.path}`\n\n```ams\n{job.get_input().rstrip()}\n```\n"
def main() -> None:
TABLES.mkdir(exist_ok=True)
FIGURES.mkdir(exist_ok=True)
setup_map = completed_jobs("01-initial-system_workdir", "setup_opt")
equilibration = sorted_cumulative_jobs(completed_jobs("02-equilibration_workdir", "eq_*ps"), "eq_")
production = sorted_cumulative_jobs(completed_jobs("03-production_workdir", "prod_*ps"), "prod_")
msd_jobs = successful_msd_jobs()
fragmentation = fragmentation_failure_paths()
if not setup_map or not equilibration or not production:
raise RuntimeError("Setup, equilibration, and production jobs must exist before rendering the report.")
setup = setup_map["setup_opt"]
final_eq_duration, final_eq = equilibration[-1]
final_prod_duration, final_prod = production[-1]
eq_table = equilibration_table(equilibration)
prod_table = production_table(msd_jobs)
eq_table.to_csv(TABLES / "equilibration-convergence.csv", index=False)
prod_table.to_csv(TABLES / "production-convergence.csv", index=False)
eq_trace = history_frame(final_eq, "equilibration")
prod_trace = history_frame(final_prod, "production")
eq_trace.to_csv(TABLES / "equilibration-trace.csv", index=False)
prod_trace.to_csv(TABLES / "production-trace.csv", index=False)
make_trace_figure(eq_trace, prod_trace)
packed_system = setup.results.get_input_system()
view(
packed_system,
guess_bonds=len(packed_system.bonds) == 0,
direction="tilt_x",
width=700,
height=700,
picture_path=str(FIGURES / "packed-system.png"),
)
final_msd: Optional[AMSMSDJob] = None
diffusion: Optional[float] = None
fit_r_squared: Optional[float] = None
if msd_jobs:
latest_msd_duration = max(msd_jobs)
final_msd = msd_jobs[latest_msd_duration]
diffusion = float(final_msd.results.get_diffusion_coefficient(
start_time_fit_fs=MSD_FIT_START_FS, end_time_fit_fs=MSD_WINDOW_FS
))
fit_result, _, _ = final_msd.results.get_linear_fit(
start_time_fit_fs=MSD_FIT_START_FS, end_time_fit_fs=MSD_WINDOW_FS
)
fit_r_squared = float(fit_result.rvalue ** 2)
make_msd_figure(final_msd)
eq_converged = bool(len(eq_table) and eq_table.iloc[-1]["accepted"])
prod_converged = bool(len(prod_table) and prod_table.iloc[-1]["converged"])
fragmentation_status = "detected" if fragmentation else "not detected"
prod_temp_mean = float(prod_trace["temperature_k"].mean())
prod_temp_std = float(prod_trace["temperature_k"].std(ddof=1))
prod_pressure_mean = float(prod_trace["pressure_pa"].mean())
prod_pressure_std = float(prod_trace["pressure_pa"].std(ddof=1))
density = setup.results.get_input_molecule().get_density() / 1000
if diffusion is None:
result_text = "No valid molecular-center-of-mass diffusion estimate was produced."
else:
result_text = (f"The final glycine center-of-mass diffusion coefficient is **{diffusion:.6e} m^2/s** "
f"with a fitted MSD R^2 of {fit_r_squared:.6f}.")
if fragmentation:
convergence_text = "The molecular-center-of-mass analysis detected a glycine bond change, so production stopped and the result is not converged."
elif prod_converged:
convergence_text = "The last three cumulative estimates are each within 15% of their mean, so the production estimate is converged by the specified test."
elif final_prod_duration >= 1000:
convergence_text = "The trajectory reached the 1 ns cap without meeting the three-estimate test. The latest estimate is reported as unconverged."
else:
convergence_text = "The available trajectory has not yet met the three-estimate convergence test."
markdown = f"""# Glycine diffusion in water at 380 K
## Result
{result_text} The MSD correlation window is 20 ps and the fitted interval is 5-20 ps. The cumulative production trajectory is {final_prod_duration} ps. {convergence_text}
The mean of the final three cumulative estimates is {float(prod_table.iloc[-1]['last_three_mean_m2_s']):.6e} m^2/s. This mean is used only for the convergence test; the reported coefficient comes from the full {final_prod_duration} ps trajectory.
The production trajectory has a mean temperature of {prod_temp_mean:.3f} +/- {prod_temp_std:.3f} K and a mean pressure of {prod_pressure_mean:.6e} +/- {prod_pressure_std:.6e} Pa. The fragmentation or atom-exchange status is **{fragmentation_status}**.
## System and protocol
The periodic cubic starting system contains one neutral NH2-CH2-COOH glycine molecule and 40 water molecules. It has {len(packed_system)} atoms and an initial packed density of {density:.6f} g/cm^3. ReaxFF used `Glycine.ff` with `nproc=1`. The geometry optimization used Basic convergence. Equilibration used Berendsen NVT at 380 K with a 100 fs coupling time. Production used a separate NHC NVT trajectory with a 100 fs coupling time. Both MD stages used a 0.5 fs timestep and stored a frame every 100 fs.
The equilibration endpoint is {final_eq_duration} ps and its convergence status is **{'accepted' if eq_converged else 'not accepted by the two-check test'}**.
## Equilibration convergence
{eq_table.to_markdown(index=False)}
The energy test fits the five block-mean potential energies over the trailing half of each accumulated trajectory. It passes when the fitted change is no more than 0.5 times the trajectory standard deviation. The temperature test requires the trailing mean to lie within 2% of 380 K. Two consecutive combined passes are required.
## Production convergence
{prod_table.to_markdown(index=False) if len(prod_table) else 'No successful center-of-mass MSD analyses were available.'}
{'' if final_msd is not None else ''}
CSV data are in [`tables/`](tables/). The convergence histories, thermodynamic traces, and MSD values shown here come directly from the individual AMS and Analysis job directories.
## Limitations
The box contains only 40 water molecules. Periodic hydrodynamic finite-size effects can therefore bias the diffusion coefficient. No finite-size correction or independent replicate trajectories were applied. The fixed-density NVT state also prevents density relaxation and makes the reported mean pressure an observation rather than a controlled state variable.
## Complete calculation inputs
"""
markdown += input_section("Initial ReaxFF geometry optimization", setup)
for duration, job in equilibration:
markdown += input_section(f"Equilibration, cumulative {duration} ps", job)
for duration, job in production:
markdown += input_section(f"Production, cumulative {duration} ps", job)
if final_msd is not None:
input_files = sorted(Path(final_msd.path).glob("*.in"))
if input_files:
markdown += f"### Final MSD analysis\n\nProvenance: `{final_msd.path}`\n\n```ams\n{input_files[0].read_text().rstrip()}\n```\n"
markdown += "\n## Conclusion\n\n" + result_text + " " + convergence_text + "\n"
(ROOT / "report.md").write_text(markdown)
log(f"Wrote {(ROOT / 'report.md')} with tables and figures.")
if __name__ == "__main__":
main()
Original Markdown report
# Glycine diffusion in water at 380 K
## Result
The final glycine center-of-mass diffusion coefficient is **1.511364e-09 m^2/s** with a fitted MSD R^2 of 0.997441. The MSD correlation window is 20 ps and the fitted interval is 5-20 ps. The cumulative production trajectory is 300 ps. The last three cumulative estimates are each within 15% of their mean, so the production estimate is converged by the specified test.
The mean of the final three cumulative estimates is 1.362155e-09 m^2/s. This mean is used only for the convergence test; the reported coefficient comes from the full 300 ps trajectory.
The production trajectory has a mean temperature of 380.189 +/- 27.099 K and a mean pressure of 3.452129e+08 +/- 6.113907e+08 Pa. The fragmentation or atom-exchange status is **not detected**.
## System and protocol
The periodic cubic starting system contains one neutral NH2-CH2-COOH glycine molecule and 40 water molecules. It has 130 atoms and an initial packed density of 1.000000 g/cm^3. ReaxFF used `Glycine.ff` with `nproc=1`. The geometry optimization used Basic convergence. Equilibration used Berendsen NVT at 380 K with a 100 fs coupling time. Production used a separate NHC NVT trajectory with a 100 fs coupling time. Both MD stages used a 0.5 fs timestep and stored a frame every 100 fs.
The equilibration endpoint is 45 ps and its convergence status is **accepted**.
## Equilibration convergence
| duration_ps | window_start_ps | window_end_ps | fitted_energy_change_hartree | energy_std_hartree | abs_change_over_std | mean_temperature_k | temperature_error_percent | energy_pass | temperature_pass | combined_pass | consecutive_passes | accepted |
|--------------:|------------------:|----------------:|-------------------------------:|---------------------:|----------------------:|---------------------:|----------------------------:|:--------------|:-------------------|:----------------|---------------------:|:-----------|
| 10 | 5 | 10 | -0.0190687 | 0.0164304 | 1.16057 | 380.343 | 0.0902924 | False | True | False | 0 | False |
| 15 | 7.5 | 15 | 0.00287543 | 0.0168213 | 0.17094 | 383.242 | 0.853122 | True | True | True | 1 | False |
| 20 | 10 | 20 | 0.0114965 | 0.0170214 | 0.675412 | 380.281 | 0.0738878 | False | True | False | 0 | False |
| 25 | 12.5 | 25 | 0.000842544 | 0.0156176 | 0.0539484 | 379.496 | 0.132534 | True | True | True | 1 | False |
| 30 | 15 | 30 | -0.0112081 | 0.0155284 | 0.721783 | 377.881 | 0.557719 | False | True | False | 0 | False |
| 35 | 17.5 | 35 | -0.0111003 | 0.0153148 | 0.724808 | 378.855 | 0.301305 | False | True | False | 0 | False |
| 40 | 20 | 40 | -0.00480942 | 0.0145039 | 0.331594 | 380.175 | 0.0461648 | True | True | True | 1 | False |
| 45 | 22.5 | 45 | 0.00470817 | 0.0153053 | 0.307618 | 380.689 | 0.181303 | True | True | True | 2 | True |
The energy test fits the five block-mean potential energies over the trailing half of each accumulated trajectory. It passes when the fitted change is no more than 0.5 times the trajectory standard deviation. The temperature test requires the trailing mean to lie within 2% of 380 K. Two consecutive combined passes are required.
## Production convergence
| duration_ps | diffusion_m2_s | last_three_mean_m2_s | last_three_max_deviation_percent | converged |
|--------------:|-----------------:|-----------------------:|-----------------------------------:|:------------|
| 100 | 1.03978e-09 | nan | nan | False |
| 150 | 9.95771e-10 | nan | nan | False |
| 200 | 1.36014e-09 | 1.1319e-09 | 20.1646 | False |
| 250 | 1.21496e-09 | 1.19029e-09 | 16.3422 | False |
| 300 | 1.51136e-09 | 1.36216e-09 | 10.9539 | True |
CSV data are in [`tables/`](tables/). The convergence histories, thermodynamic traces, and MSD values shown here come directly from the individual AMS and Analysis job directories.
## Limitations
The box contains only 40 water molecules. Periodic hydrodynamic finite-size effects can therefore bias the diffusion coefficient. No finite-size correction or independent replicate trajectories were applied. The fixed-density NVT state also prevents density relaxation and makes the reported mean pressure an observation rather than a controlled state variable.
## Complete calculation inputs
### Initial ReaxFF geometry optimization
Provenance: `/home/ubuntu/work/01-initial-system_workdir/setup_opt`
```ams
GeometryOptimization
Convergence
Quality Basic
End
End
Task GeometryOptimization
System
Atoms
N 1.2281940000 7.1738140000 7.3324350000 region=glycine
C 2.5627490000 7.3379360000 7.8363910000 region=glycine
C 2.6378550000 7.5441720000 9.2925960000 region=glycine
O 1.6426130000 7.4817520000 10.0719620000 region=glycine
O 3.8740130000 7.9426300000 9.8084330000 region=glycine
H 1.2580100000 7.3712460000 6.3017280000 region=glycine
H 0.9461930000 6.1688350000 7.4105530000 region=glycine
H 3.0316870000 8.1755850000 7.2622640000 region=glycine
H 3.1888220000 6.4463850000 7.5799160000 region=glycine
H 4.7592150000 7.6221990000 9.4594070000 region=glycine
O 2.8743300000 4.8500010000 5.4275130000 region=water
H 3.7118750000 5.3221630000 5.2365690000 region=water
H 2.1693960000 5.4632870000 5.7294450000 region=water
O 9.5338540000 4.9835590000 9.8024440000 region=water
H 9.9680140000 4.4902400000 9.0751060000 region=water
H 9.9735900000 5.8446590000 9.9737720000 region=water
O 4.2904420000 1.1762610000 9.9876590000 region=water
H 3.4023330000 0.9942730000 9.6148020000 region=water
H 5.0047950000 0.9814380000 9.3427110000 region=water
O 4.2805610000 2.3894080000 5.7250290000 region=water
H 3.5480290000 2.8887250000 6.1433090000 region=water
H 4.9137390000 2.9840080000 5.2670440000 region=water
O 3.1201750000 4.2431350000 3.3282950000 region=water
H 2.1677470000 4.4685780000 3.3824840000 region=water
H 3.2687430000 3.2730100000 3.3599170000 region=water
O 1.0350490000 1.0933760000 3.7970630000 region=water
H 1.1849970000 2.0222430000 3.5221080000 region=water
H 1.0032430000 1.0018090000 4.7742110000 region=water
O 1.7588500000 2.5525240000 9.4261730000 region=water
H 1.9241970000 3.3640490000 9.9505460000 region=water
H 1.3032860000 1.8618730000 9.9550190000 region=water
O 3.7777050000 9.4109060000 5.6032650000 region=water
H 4.5727600000 9.9835680000 5.6319810000 region=water
H 2.9480700000 9.9359880000 5.6177340000 region=water
O 9.3199090000 8.2892990000 3.1125280000 region=water
H 8.9793070000 7.5576830000 2.5561040000 region=water
H 8.6037300000 8.9002450000 3.3919000000 region=water
O 9.5978570000 9.1395960000 8.3427440000 region=water
H 9.8069050000 8.1820350000 8.3267630000 region=water
H 9.1668250000 9.4337620000 7.5109440000 region=water
O 6.8855070000 3.9843750000 3.9838930000 region=water
H 7.5338410000 3.7983390000 3.2726030000 region=water
H 5.9652130000 4.0098670000 3.6423920000 region=water
O 3.4688030000 5.1630140000 10.0021910000 region=water
H 2.7002820000 5.3537330000 9.4243660000 region=water
H 4.3082360000 5.4949840000 9.6157170000 region=water
O 6.8937070000 7.6877530000 1.7415270000 region=water
H 7.4386890000 7.3504620000 0.9998340000 region=water
H 6.0009320000 7.9662860000 1.4422150000 region=water
O 1.7598440000 0.9837060000 7.1327360000 region=water
H 1.4321260000 1.8795720000 7.3583550000 region=water
H 2.4476560000 1.0115050000 6.4324810000 region=water
O 4.1997220000 3.4776740000 8.7527800000 region=water
H 4.6084860000 3.3218650000 9.6300000000 region=water
H 4.0288850000 2.6372980000 8.2744510000 region=water
O 3.1328560000 10.0060880000 8.7831480000 region=water
H 3.0323260000 9.9747400000 9.7577200000 region=water
H 4.0216830000 9.7020520000 8.4972050000 region=water
O 7.6429470000 6.4648490000 9.9754570000 region=water
H 8.2659810000 7.2216230000 9.9761680000 region=water
H 6.7069550000 6.7617160000 9.9739300000 region=water
O 1.1238710000 7.3330540000 3.5435330000 region=water
H 1.7100530000 6.6146260000 3.8615420000 region=water
H 0.9950830000 8.0284910000 4.2247060000 region=water
O 3.1711510000 9.4228500000 3.4904940000 region=water
H 3.9847110000 9.9696440000 3.4868070000 region=water
H 2.3593370000 9.9751680000 3.5013810000 region=water
O 3.4498030000 7.8083110000 1.4650990000 region=water
H 3.8632030000 7.0535670000 0.9956940000 region=water
H 2.8233570000 7.5084470000 2.1592620000 region=water
O 9.9723070000 3.2471620000 4.1010420000 region=water
H 9.7026170000 4.0052240000 3.5411420000 region=water
H 9.7762750000 2.3866170000 3.6706370000 region=water
O 1.1847490000 9.2145870000 8.1480430000 region=water
H 0.9941810000 9.5632080000 9.0441610000 region=water
H 0.9987840000 9.8794660000 7.4497820000 region=water
O 5.5152160000 2.1951010000 1.8362650000 region=water
H 6.0909770000 2.0777250000 2.6208670000 region=water
H 6.0269930000 2.1622210000 0.9988770000 region=water
O 4.2847400000 7.4837140000 4.6872470000 region=water
H 5.1608280000 7.9146060000 4.7748920000 region=water
H 4.1840880000 7.0325960000 3.8208890000 region=water
O 7.4123570000 4.0310040000 6.3218290000 region=water
H 6.5495100000 3.6288330000 6.5555640000 region=water
H 7.3388210000 5.0005640000 6.1848560000 region=water
O 5.7067250000 4.8279570000 0.9995700000 region=water
H 5.1071620000 4.7922320000 1.7742490000 region=water
H 6.6347100000 4.6216190000 1.2455040000 region=water
O 5.2963200000 5.5925530000 6.7352960000 region=water
H 5.2311150000 6.5689220000 6.7929970000 region=water
H 4.9476720000 5.1544260000 7.5419580000 region=water
O 6.2306090000 6.2425450000 3.6556510000 region=water
H 6.1664930000 5.9676770000 4.5943820000 region=water
H 7.1497980000 6.1753050000 3.3168510000 region=water
O 2.4362630000 4.3326510000 0.9611220000 region=water
H 2.8296630000 5.1439010000 1.3458130000 region=water
H 2.9471600000 3.5291710000 1.2011620000 region=water
O 6.7782980000 1.7758440000 8.3161120000 region=water
H 7.1350590000 0.9981570000 8.7944460000 region=water
H 7.4593280000 2.4720120000 8.1905540000 region=water
O 4.0403210000 1.2242650000 3.1486030000 region=water
H 4.3717030000 0.9820800000 4.0387770000 region=water
H 3.0945060000 0.9868340000 3.0333770000 region=water
O 9.9753760000 5.9936110000 4.5959620000 region=water
H 9.0696320000 6.3021160000 4.3830490000 region=water
H 9.9719860000 5.3041600000 5.2951470000 region=water
O 6.5718080000 9.3078860000 6.1595700000 region=water
H 6.9689030000 9.9751830000 6.7578240000 region=water
H 6.8836870000 9.4143460000 5.2345770000 region=water
O 9.5890600000 2.3236390000 9.6084840000 region=water
H 8.8423730000 2.8441540000 9.9723540000 region=water
H 9.2874010000 1.4737850000 9.2199420000 region=water
O 8.8977610000 2.2830250000 6.5417060000 region=water
H 9.4518700000 3.0631070000 6.7545790000 region=water
H 8.6982760000 2.2270900000 5.5818660000 region=water
O 8.7041910000 2.3434330000 1.2535510000 region=water
H 9.1466590000 3.1496010000 1.5929530000 region=water
H 9.3516940000 1.6503050000 0.9995270000 region=water
O 1.5713830000 4.0989480000 7.8049630000 region=water
H 2.5122130000 4.2112950000 7.5537730000 region=water
H 0.9911510000 4.0076630000 7.0180630000 region=water
O 7.2924750000 7.6521450000 8.0508440000 region=water
H 6.5943890000 8.2828490000 8.3261020000 region=water
H 7.2286710000 7.4295900000 7.0965830000 region=water
O 7.2240600000 4.2529950000 9.4589840000 region=water
H 6.5947550000 4.8138900000 8.9587330000 region=water
H 6.7625820000 3.5579990000 9.9768950000 region=water
O 9.1683180000 5.7433810000 7.4569070000 region=water
H 8.3489470000 5.7251700000 7.9946610000 region=water
H 9.2466430000 6.5731420000 6.9376990000 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 5 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_005ps`
```ams
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
InitialVelocities
Temperature 380.0
Type Random
End
NSteps 10000
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 1.3482433945 7.1933736074 7.2825879312 region=glycine
C 2.7432713754 7.5023634327 7.7575110950 region=glycine
C 2.8365986194 7.7589518236 9.2741683520 region=glycine
O 1.8746954418 8.0240812926 9.9247898874 region=glycine
O 4.1174562420 7.7611240843 9.8194363666 region=glycine
H 1.2813659396 7.1640118916 6.2631253604 region=glycine
H 1.0280970197 6.2558918755 7.5816979078 region=glycine
H 3.1187686566 8.4152625655 7.1735509973 region=glycine
H 3.3879753123 6.6436741148 7.4558438321 region=glycine
H 4.6556940492 7.6097369324 8.9955912555 region=glycine
O 2.7175951668 4.9630258436 5.1423395010 region=water
H 3.4333355935 5.6207939739 5.3223231106 region=water
H 2.2335750662 4.8301479402 5.9972324189 region=water
O 10.0433002022 4.9267499529 10.2481504640 region=water
H 10.3161733871 5.1461512101 9.3593903348 region=water
H 9.2108291708 5.4013551420 10.3271471342 region=water
O 4.8055139039 1.7216141013 9.9364737017 region=water
H 4.1054818113 1.0074413397 9.7831100348 region=water
H 5.6400679047 1.3790991470 9.4576572308 region=water
O 4.5855160614 2.4867357891 5.6134097054 region=water
H 3.9968917174 3.2562245443 5.4924859259 region=water
H 5.4152499765 2.7828990779 5.1718150277 region=water
O 3.8384979254 4.0109415177 2.8039249673 region=water
H 3.4169452437 4.3692789325 3.6231846096 region=water
H 3.9246882561 2.9999025011 2.9446936666 region=water
O 1.2227729859 1.1071958565 4.1046707360 region=water
H 0.5697189005 1.7990443326 3.8598786187 region=water
H 1.3302454144 1.1966981566 5.0754937776 region=water
O 1.2417768262 2.1428225427 9.7355640571 region=water
H 1.4742704719 2.5086844993 10.6042523688 region=water
H 0.2673152706 1.9793984299 9.7590616004 region=water
O 3.6651769497 9.9752499618 6.2924367070 region=water
H 4.6213413436 9.8313408792 6.1350948660 region=water
H 3.2253185988 9.7576402956 5.4162565047 region=water
O 9.0070436177 8.2980951037 3.4247888386 region=water
H 9.6237182146 8.1021724258 2.7182921002 region=water
H 8.1497849567 8.3187303214 2.9660997621 region=water
O 9.0022870595 8.7681105380 8.2785209820 region=water
H 9.9679985667 8.8688653439 8.2740519691 region=water
H 8.7265233157 9.6403356603 7.9857378795 region=water
O 6.6259062387 3.2827919746 3.7925032772 region=water
H 7.1074860347 2.8735008379 3.0678634757 region=water
H 5.9681665056 3.7965046280 3.3176501229 region=water
O 2.8354319921 4.9696298790 10.3104966013 region=water
H 2.4909076414 4.6648716858 9.4733046101 region=water
H 3.7409883287 5.1831355388 10.0899058417 region=water
O 6.7423777913 8.4385279151 1.5434309480 region=water
H 7.1800440359 7.9162021193 0.8368988422 region=water
H 5.8595810182 8.0492320254 1.6554173820 region=water
O 1.8217549328 1.5187192485 6.8935013216 region=water
H 1.8526082005 1.6490568343 7.8536747992 region=water
H 2.7390299082 1.3432181716 6.6690560225 region=water
O 4.1968582856 3.6112197439 8.1697547875 region=water
H 4.3262143498 3.0077863767 8.9730867716 region=water
H 4.4142673832 3.0561900967 7.3969304618 region=water
O 3.2914924758 10.6913796602 9.0413825439 region=water
H 3.3913963780 9.8544125607 9.5068703754 region=water
H 3.5510672390 10.4934769801 8.1224366365 region=water
O 8.0444648209 7.1231753810 10.4056132151 region=water
H 8.5253218825 7.8061688060 9.9077743822 region=water
H 7.3505322101 6.8462004104 9.7999099221 region=water
O 1.6334725326 7.1318079621 3.2243983355 region=water
H 2.0676721973 6.6086791244 3.9142411776 region=water
H 1.8094099854 8.0531085465 3.4789959248 region=water
O 2.6573725274 9.7321509480 3.7858961790 region=water
H 3.3510817538 10.2801766230 3.3863506732 region=water
H 1.9050595424 10.3524156537 3.8576062359 region=water
O 3.9473591331 7.4410297304 1.7573373702 region=water
H 3.7993530372 7.5369249147 0.8048635076 region=water
H 3.0512724236 7.2718922496 2.1376737555 region=water
O 10.1857546009 3.0177527630 4.1040457642 region=water
H 10.0197211445 3.9542801225 4.3189778301 region=water
H 9.7801096557 2.8907724840 3.2181768583 region=water
O 0.4407691610 10.0467538449 7.7182514162 region=water
H 0.9962343135 9.3137426657 7.9855204896 region=water
H 1.0557503247 10.7766808652 7.5813221002 region=water
O 5.9621390329 2.0952665762 1.4478166938 region=water
H 5.3562823311 1.9449003334 2.1932786508 region=water
H 5.4163753607 1.9421822991 0.6436596654 region=water
O 4.0842864618 7.3422481208 4.8717977717 region=water
H 5.0112626466 7.5593685350 4.9758932378 region=water
H 3.9795900317 7.4323213775 3.9231022481 region=water
O 7.1214205493 3.5192211020 7.0477676855 region=water
H 6.2254146695 3.5124341915 6.6856020697 region=water
H 7.3884256085 4.4167355901 6.8129520810 region=water
O 5.7816382522 4.7646071931 0.9577622246 region=water
H 5.0922203615 5.0989972503 1.5524093829 region=water
H 5.9502457210 3.8355916323 1.2682266520 region=water
O 5.3188597972 5.4025490990 6.3474716708 region=water
H 5.4801194310 6.3049655780 6.6631558859 region=water
H 4.9593774357 4.9252837075 7.1226191783 region=water
O 6.7097187967 6.3617931999 3.9847866465 region=water
H 6.2070854522 5.8776128516 4.6526056429 region=water
H 7.6334515824 6.0409203753 4.0531268176 region=water
O 1.7006732139 3.5132916247 1.2777129156 region=water
H 1.8079973321 4.1878380385 0.5696500340 region=water
H 2.4300931953 3.7282008750 1.9408651815 region=water
O 6.9266347866 0.8719436332 8.5105140057 region=water
H 7.6902211141 1.0322322101 9.0927737898 region=water
H 6.9716870124 1.6336564074 7.9122002070 region=water
O 3.8198087581 1.3873775969 3.2876114084 region=water
H 4.1919538908 1.5381251717 4.2094882642 region=water
H 2.8284068743 1.3267386725 3.4135114002 region=water
O 9.3581063686 5.7550823097 4.5409584399 region=water
H 9.4250389923 6.6745946454 4.1895931695 region=water
H 9.3739279237 5.8360980618 5.5194415475 region=water
O 6.4141630106 9.5171505643 5.7853374231 region=water
H 6.7865028806 10.2402525523 6.2915498274 region=water
H 7.0946603466 9.3722557560 5.1276920888 region=water
O 9.4904045942 1.8060314024 9.5886840853 region=water
H 9.1209585966 2.7061278958 9.6943354965 region=water
H 9.6210396612 1.7181246862 8.6191794448 region=water
O 9.5524202357 2.0064989195 6.7550917550 region=water
H 8.6731159291 2.4033975239 6.6731406190 region=water
H 9.9990406844 2.2441334141 5.9308191575 region=water
O 9.2080589431 2.7754060335 1.4475982879 region=water
H 9.4364205764 3.5073479180 0.8673693423 region=water
H 9.2503552288 2.0425343529 0.8344589090 region=water
O 1.4560043528 4.3322934490 7.5261158871 region=water
H 2.3341796474 3.9942770598 7.7928914672 region=water
H 0.9999960026 3.5142385117 7.2718611218 region=water
O 6.1833343525 7.5976729493 7.8923754927 region=water
H 7.0207511492 7.8043837451 8.3310480725 region=water
H 6.1588539970 8.2483691277 7.1630835144 region=water
O 7.4663508388 3.9410713824 9.6838202121 region=water
H 6.9948997708 3.6894833732 8.8655559377 region=water
H 6.7873742435 4.1229910377 10.3481293489 region=water
O 9.1680836121 5.8585453044 7.3877689735 region=water
H 8.5956916508 5.3515787859 7.9671346593 region=water
H 9.0539887958 6.7620706429 7.7000117621 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 10 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_010ps`
```ams
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_005ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 20000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_005ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 4.6694817673 4.4382242179 9.1209929138 region=glycine
C 5.2927837313 5.8318224333 9.1635611385 region=glycine
C 4.8582260597 6.8107612168 10.2808212578 region=glycine
O 4.5716111299 6.4682367410 0.4024492826 region=glycine
O 5.3122724729 8.1541812953 10.0517910437 region=glycine
H 4.7935746200 4.0255649383 8.1231082087 region=glycine
H 5.2197031650 3.7522367487 9.7237522662 region=glycine
H 4.9912366237 6.2568904897 8.1689840732 region=glycine
H 6.4418520652 5.7248768675 9.0578857765 region=glycine
H 5.1052368978 8.2204225890 9.1219837639 region=glycine
O 7.1338406900 8.2812728733 3.2921588005 region=water
H 7.4828162991 7.5470149600 3.8319922898 region=water
H 6.6084695560 8.8469719932 3.8157826856 region=water
O 10.6645294568 2.3644221720 7.5740591978 region=water
H 0.4642831260 1.9553881148 7.3103747279 region=water
H 10.3867753329 1.7523158636 8.2922497915 region=water
O 3.7653514742 1.2391848005 2.0495672009 region=water
H 2.8770138701 0.9547469682 1.9432174330 region=water
H 3.7972812566 1.7946894383 2.8543990431 region=water
O 2.0748089742 8.9021389344 4.8341056331 region=water
H 2.6425407006 8.0966442282 4.8161977714 region=water
H 2.6646916325 9.5693806611 5.1805835689 region=water
O 1.6976848093 3.7776437761 1.5090056353 region=water
H 1.6586987506 3.6527813381 0.5640180226 region=water
H 1.1966600908 4.5584599387 1.7217208980 region=water
O 0.1593426578 4.1125292260 4.3090250318 region=water
H 10.6528316652 4.9233457473 4.3273699227 region=water
H 0.9601848049 4.3967618584 4.8518157601 region=water
O 4.9633576666 2.9215802034 6.6896581350 region=water
H 5.8820571426 2.8679621463 6.3365460027 region=water
H 4.8264628714 2.0283136781 6.7165565678 region=water
O 10.7157513939 5.6617775319 1.0260253912 region=water
H 10.6600695891 5.6850865169 0.0236035170 region=water
H 10.9527607418 6.5673745787 1.3132356946 region=water
O 5.0684135303 3.7990339439 3.9749060984 region=water
H 4.9879161863 3.2813622953 4.7844345896 region=water
H 4.4646830353 3.4303190599 3.3158120057 region=water
O 5.3309915710 7.7414704646 6.8781976348 region=water
H 4.4913157906 7.9026228087 6.4605540432 region=water
H 6.0490344515 7.7680697997 6.2505421865 region=water
O 1.1157495109 0.1574676414 1.2703635949 region=water
H 0.8590459620 0.3250305126 2.2031705035 region=water
H 0.4657331787 0.5824480443 0.6851357522 region=water
O 8.4247459540 1.9318872882 4.8164183309 region=water
H 9.2582461283 1.5245650675 4.8802121219 region=water
H 8.5456005249 2.6069207147 4.1279859540 region=water
O 8.1187920961 1.0570928202 0.3053202949 region=water
H 7.4541025407 1.4177238520 10.5882315766 region=water
H 7.7774908527 0.1513836830 0.4695977472 region=water
O 2.3326872723 1.2482041689 5.8422317338 region=water
H 3.2351249242 0.8859356300 5.5977797279 region=water
H 2.3859792023 1.3898413274 6.8201669750 region=water
O 4.6523554579 10.8009432497 5.7721953686 region=water
H 5.2867619957 10.8228424856 5.0662952558 region=water
H 5.1292896758 10.6085943826 6.5835421821 region=water
O 4.0389590298 7.1386005131 3.5977597940 region=water
H 4.9184290017 7.4344225303 3.7708177483 region=water
H 4.1720741651 6.5720641346 2.8813838876 region=water
O 8.1370379933 9.9999759556 7.2888013756 region=water
H 7.8771295877 9.0466426027 7.0397630389 region=water
H 8.7345031325 10.4127626381 6.6336367406 region=water
O 10.0656503243 10.4199569500 5.0869973451 region=water
H 10.6446317826 9.6539906607 4.8718236155 region=water
H 10.3930912061 0.2201131071 4.5684359281 region=water
O 2.5431151193 0.9684700723 8.4501159472 region=water
H 2.1618357467 0.1159180750 8.2617772273 region=water
H 3.3445843510 0.7779100516 8.9564082418 region=water
O 4.2604624764 10.8828558955 10.6184603770 region=water
H 4.1781301092 9.8333832238 10.5366180693 region=water
H 3.8013785963 0.1424933606 0.4621730042 region=water
O 9.0775276640 3.7103894239 2.5529470108 region=water
H 8.6940421680 4.0334078450 1.7778689108 region=water
H 9.9466097056 3.9220095026 2.3652616223 region=water
O 1.8807202054 9.2973254437 8.2431474946 region=water
H 2.0775219801 8.4653127770 7.7659523821 region=water
H 1.7951621259 9.1446189472 9.1828549000 region=water
O 10.4319183153 0.5267979579 10.1279761546 region=water
H 9.6375710850 0.9026166782 10.6497197526 region=water
H 10.1761276391 10.5196353848 9.8750818206 region=water
O 8.4912392399 7.5071687205 6.4496433666 region=water
H 9.2284527240 7.8560412425 5.9994018879 region=water
H 8.0473834460 7.0233739111 5.7184114987 region=water
O 9.7186275501 5.1416499563 7.7811311655 region=water
H 9.5152586133 5.6797209833 7.0218152321 region=water
H 9.9449753427 4.2785377121 7.4867974296 region=water
O 7.3706584181 9.2865406038 0.5138975475 region=water
H 6.5215556686 8.9380407533 0.1589565617 region=water
H 7.2160912926 9.0756790959 1.4759783012 region=water
O 5.8829839594 1.9541670924 9.7626679328 region=water
H 5.9302406738 1.7029708954 8.7810228974 region=water
H 4.9927928546 1.5971865119 10.0791764040 region=water
O 10.7628203583 7.8726173444 4.5313520510 region=water
H 10.9687416470 8.0338091844 3.6295485138 region=water
H 0.6551195239 7.9410195787 4.9983379116 region=water
O 7.5737014536 5.8314489999 4.3450665226 region=water
H 6.8539873473 5.3498459332 3.9476177328 region=water
H 8.2571606224 5.4468593458 3.7981392937 region=water
O 6.3155459715 10.9377883092 3.5996893713 region=water
H 5.8104191794 0.3887993636 2.8834992229 region=water
H 7.0550156207 0.5049852342 3.7776265067 region=water
O 0.4930190941 8.2247702798 1.8847114471 region=water
H 0.1274170817 9.1364694766 1.5562039237 region=water
H 1.2254450881 8.5112453812 2.5397394606 region=water
O 0.3450308302 1.4735420754 3.5601895859 region=water
H 1.1544398155 1.4577465799 4.0949123165 region=water
H 0.1060316403 2.4028204511 3.6702583421 region=water
O 2.7534426314 8.5788111581 0.5670875459 region=water
H 3.2910732214 8.1898179026 1.2542034655 region=water
H 2.2708580149 9.2158333089 1.0647033659 region=water
O 9.4983463013 8.9954407495 9.7510492440 region=water
H 8.8195316470 9.3392373230 9.0988056316 region=water
H 8.9394573574 8.9386357872 10.5863154397 region=water
O 7.7474894254 1.9166705642 7.7329175373 region=water
H 7.9515632866 0.9657989920 7.8670203468 region=water
H 8.5779382046 2.2247893995 7.4343130907 region=water
O 2.5960248118 6.7447772999 7.7631484655 region=water
H 2.2585020058 6.3588258099 8.5469495211 region=water
H 2.4481231680 6.0818953059 7.0610210289 region=water
O 2.2925573999 3.6669877963 9.5203756563 region=water
H 2.2534884572 2.8090415445 9.1607396709 region=water
H 3.1949787114 4.1546959599 9.3969314166 region=water
O 0.1664142529 6.7406296198 9.3586913333 region=water
H 10.8508652541 6.1884325024 8.5825444792 region=water
H 10.6876341749 7.6030269632 9.3581242937 region=water
O 2.7049149016 4.8295736737 5.6636129441 region=water
H 3.1763086096 4.1556449316 6.1399923377 region=water
H 3.3329399542 4.9270104566 4.9662543560 region=water
O 7.8421800686 4.6172584365 9.9135930563 region=water
H 7.3822511999 3.7785204888 9.7475030841 region=water
H 8.4525502292 4.8805664245 9.1816740116 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0 0 0 1
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0 1 0 0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0 -1 0 0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0 0 0 -1
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0 0 1 0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0 0 1 1
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0 0 -1 0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0 1 0 0
95 96 1.0
95 97 1.0
98 99 1.0 0 1 0
98 100 1.0 0 1 0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0 -1 0 0
122 124 1.0 -1 0 0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 15 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_015ps`
```ams
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_010ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 30000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_010ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.1147542749 6.0176060194 8.2285985240 region=glycine
C 2.8468251535 6.6149948048 9.3962728167 region=glycine
C 2.8192966761 8.1331308340 9.4108380383 region=glycine
O 2.0819826563 8.7904362537 8.6893539203 region=glycine
O 3.5453126542 8.6371445187 10.4115344718 region=glycine
H 2.2747581712 5.0068139657 7.9769573805 region=glycine
H 2.2095342091 6.5937535898 7.3737371409 region=glycine
H 3.8889957255 6.1890710341 9.5079614506 region=glycine
H 2.2234242639 6.3306811015 10.4021488948 region=glycine
H 4.1246791113 7.8418034680 10.7550373248 region=glycine
O 5.6873558067 7.0265628109 3.0322670412 region=water
H 5.1745840684 7.8169790371 3.3135432734 region=water
H 5.7963493324 7.0163788906 2.0782578012 region=water
O 8.9306064130 3.1367712868 7.2331484785 region=water
H 9.0714318637 3.4550990885 8.1376849727 region=water
H 7.9817762092 3.0790338914 7.2257250241 region=water
O 0.3977825929 8.2433821682 4.0311172834 region=water
H 0.5497316147 9.2452205682 4.1493593353 region=water
H 10.6090325998 8.0905395510 3.5252968830 region=water
O 3.3486600222 4.7202829960 1.7375499065 region=water
H 2.5950402267 5.2894405255 1.6149519107 region=water
H 3.5462243736 4.5978768869 2.8052044007 region=water
O 0.1739304460 10.1020757518 0.5920333829 region=water
H 10.8974227614 9.2141821917 0.3426109216 region=water
H 1.0699852470 10.0351835207 0.9565348018 region=water
O 9.7931195255 4.6057565169 2.6700733286 region=water
H 8.9062295934 4.2245169500 2.6396628873 region=water
H 9.7023481933 5.4360712560 2.2199879034 region=water
O 6.2329049051 4.0061675392 6.2429772061 region=water
H 6.6568244716 4.6687923124 5.6753216821 region=water
H 6.1082351933 4.6447623172 7.0121888238 region=water
O 9.7358872787 7.4547113777 1.9059738671 region=water
H 9.7243798901 7.5968940206 0.9281641758 region=water
H 9.2477611828 8.2072245717 2.2161494967 region=water
O 4.7269501141 1.3902019985 5.6993350990 region=water
H 4.8631190900 1.0512898405 6.5937818185 region=water
H 5.0531527874 2.3314882327 5.7774788585 region=water
O 5.4394563836 6.4133416669 0.4733185914 region=water
H 6.2528403375 6.3194531812 10.8972146266 region=water
H 4.9837668656 5.5711452904 0.3029854703 region=water
O 2.8010881312 0.1602373421 1.7677233517 region=water
H 2.0245508903 0.5155762354 2.1123049665 region=water
H 3.0920481153 10.4829771400 2.3324410376 region=water
O 9.3777839951 1.7820230635 3.5398885260 region=water
H 9.5082975230 2.6036508483 3.1773123194 region=water
H 8.4229974593 1.5490921345 3.5331278367 region=water
O 5.4218073647 1.0430197594 0.5629384968 region=water
H 4.8573705716 1.6619061982 0.0703277858 region=water
H 4.9302308075 0.5015535964 1.1538088071 region=water
O 4.3158133309 3.2554977198 10.5195368693 region=water
H 3.9796084221 3.6916757899 0.4178254307 region=water
H 3.4564920552 3.1997084735 9.9816916742 region=water
O 0.7065144310 10.9046241856 3.9772825518 region=water
H 0.0155435833 0.2991483254 3.4390322358 region=water
H 0.8316401986 0.5029880099 4.7544617765 region=water
O 10.4415243215 7.8750429721 10.0883267155 region=water
H 10.9440196072 8.2290875481 9.4028448070 region=water
H 9.7015771788 7.6241033482 9.6139660912 region=water
O 5.1216486446 8.0753370366 6.8068572065 region=water
H 4.1643126739 8.1937755482 6.5354826357 region=water
H 5.2448570444 8.7598958958 7.4835701362 region=water
O 9.2884574520 3.7247525545 10.2591788472 region=water
H 8.7429080493 3.6346978699 0.0946376543 region=water
H 9.7002463400 2.8115112421 10.1924660670 region=water
O 1.9176390438 0.5422285625 8.5251859676 region=water
H 1.1456609327 0.8396697168 9.0674987998 region=water
H 1.8779713221 10.5471595262 8.5379618737 region=water
O 10.5657739174 0.9935335288 9.7907971390 region=water
H 10.1768320970 0.6176973052 8.9306742339 region=water
H 10.6701589567 0.2170809678 10.4663620180 region=water
O 9.1794359894 8.4306017312 5.7795353651 region=water
H 9.9714571413 8.3767607903 5.2349327025 region=water
H 8.6893524506 7.6232270217 5.7333434514 region=water
O 4.7845105477 10.8194440755 8.1353846329 region=water
H 5.3104607256 0.5982967756 8.5350062857 region=water
H 3.8451198822 0.0218526435 8.4125877351 region=water
O 1.4633469067 3.2959430701 9.9403013666 region=water
H 1.5140701497 3.5798215191 9.0008615301 region=water
H 1.1309872357 2.4429969502 9.8263069927 region=water
O 5.5270691688 5.7765029409 8.4377515445 region=water
H 6.5294046349 5.7778984287 8.8207985688 region=water
H 5.4044354227 6.5816071572 7.8690119071 region=water
O 10.6450086679 4.2467607235 5.3535284613 region=water
H 10.4471529633 4.1966281030 4.3818935834 region=water
H 9.8175625322 4.0023064464 5.8170086639 region=water
O 6.5713512389 9.0985272555 10.8192236392 region=water
H 5.9225104115 8.4057449625 10.9723713839 region=water
H 6.0273937031 9.8823929167 10.8674730977 region=water
O 7.9818765558 9.8283255990 2.3708759163 region=water
H 7.4694738181 9.6917214219 1.6080611654 region=water
H 7.6303919258 10.5259405024 2.8878521387 region=water
O 1.1951471787 6.2753158505 0.9841870271 region=water
H 0.3819942297 5.9218269262 1.4183572150 region=water
H 0.7093358266 6.7137475371 0.2346981108 region=water
O 7.1634906431 6.3234238359 5.6011000607 region=water
H 6.8557072140 6.6984495362 4.7367714390 region=water
H 6.4092809086 6.7206269314 6.0784750868 region=water
O 9.9028472010 6.3727699684 7.4246008169 region=water
H 9.8807054415 5.7391066958 6.6277599440 region=water
H 9.9432767728 7.3420013519 7.0658525644 region=water
O 5.9197909796 2.2389985051 8.4812212175 region=water
H 5.6924942134 2.9589196475 7.7638580507 region=water
H 5.6846790702 2.6858835771 9.3462696399 region=water
O 3.9273215765 4.6673753847 4.6526498388 region=water
H 3.5615264782 5.3906977517 5.1296703419 region=water
H 4.7598392914 4.3527110194 5.1433730905 region=water
O 4.1368196247 9.2059406544 3.9379341738 region=water
H 4.6371444123 9.0334016740 4.7215735363 region=water
H 3.1932695957 9.0673905351 4.0763610702 region=water
O 9.3367553405 10.7443239053 7.5282238982 region=water
H 8.5718472852 0.3191065770 7.6216254873 region=water
H 9.1114137477 10.2564780305 6.7717934096 region=water
O 6.5443282708 1.0221868886 3.5938691448 region=water
H 5.9185975072 0.9553200813 4.3126760396 region=water
H 6.0477986658 1.1723400999 2.7897212294 region=water
O 1.7618550002 3.6040194676 7.0042076859 region=water
H 0.9647179636 3.9420208189 6.5884419062 region=water
H 2.0533963886 2.7007332873 6.6051071107 region=water
O 2.3129766434 6.7995174399 5.5305363335 region=water
H 1.6555173533 6.0547610625 5.4041950734 region=water
H 1.7842712108 7.5725546172 5.2526284994 region=water
O 7.9403466948 6.2530282440 9.5030912901 region=water
H 8.3512141860 5.4840727220 9.8526172867 region=water
H 8.3848023249 6.4444126878 8.6422928670 region=water
O 1.9797983523 1.1803783342 5.9242764219 region=water
H 3.0283925332 1.1876898133 5.7774385824 region=water
H 1.9137644630 0.8679226760 6.9274337850 region=water
O 7.1468186287 3.7110607279 1.2312915314 region=water
H 6.8385511526 2.8606630729 0.6994164224 region=water
H 6.2761200067 3.9974216397 1.5237493470 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0 -1 0 0
20 21 1.0
20 22 1.0
23 24 1.0 -1 0 0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0 0 0 -1
38 40 1.0
41 42 1.0
41 43 1.0 0 -1 0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0 0 0 1
50 52 1.0
53 54 1.0 0 1 0
53 55 1.0 0 1 0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0 0 0 1
62 64 1.0
65 66 1.0
65 67 1.0 0 -1 0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0 0 1 0
74 76 1.0 0 1 0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0 0 1 0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 20 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_020ps`
```ams
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_015ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 40000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_015ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.4027999254 7.1346402935 6.8166805966 region=glycine
C 3.2991967373 8.2822598660 6.4614094648 region=glycine
C 3.8303228964 9.0750725491 7.6608447173 region=glycine
O 4.2044641671 10.1914881994 7.5031679613 region=glycine
O 3.9563542669 8.4478875562 8.8461761116 region=glycine
H 2.8563595757 6.2169804735 7.1185242561 region=glycine
H 1.5005790327 7.3612999433 7.2590503779 region=glycine
H 2.8678729832 9.0666469918 5.7243693883 region=glycine
H 4.1611543900 7.7776490535 6.0207818100 region=glycine
H 3.3969362988 7.6409812514 8.7559751842 region=glycine
O 8.6830661219 6.2158917227 2.2508661795 region=water
H 9.5796596503 6.0950359094 2.0919139872 region=water
H 8.2658218623 6.8435367648 1.5688397858 region=water
O 10.7098814503 3.9592951791 7.0513995992 region=water
H 10.4046011156 4.1090420306 6.1214362125 region=water
H 10.1715750254 4.6545712869 7.5044123921 region=water
O 10.5037940320 6.4143642753 4.9218236023 region=water
H 10.9076975365 6.2607888475 4.0495719590 region=water
H 10.3225449009 7.3576528651 4.8459833684 region=water
O 4.9322668305 6.4097185683 0.5001727650 region=water
H 4.2601367636 6.1975092254 10.7950535548 region=water
H 4.4016542264 7.1075014440 1.0039676778 region=water
O 1.4060463354 0.8253965994 7.8360489525 region=water
H 1.7871897150 1.5036161488 8.3573478871 region=water
H 2.1722345393 0.2994606294 7.7835056190 region=water
O 6.1966786406 4.9336782301 2.7102436769 region=water
H 5.8445238851 5.5014539285 1.9954785333 region=water
H 7.2049561914 4.8985299026 2.4826729906 region=water
O 5.9099939199 3.3119010646 6.7035862162 region=water
H 6.4474814770 2.8024902824 7.4100349631 region=water
H 5.6488051810 4.1440683874 7.1997032958 region=water
O 9.1626100282 3.6509882322 4.4395674922 region=water
H 9.3326486149 4.5255025323 4.1155010907 region=water
H 8.2194033570 3.3473919058 4.4813204851 region=water
O 2.5720012756 2.7480316536 10.4229628815 region=water
H 3.4696971300 2.5112401182 10.4474151717 region=water
H 2.5334842677 3.7521062299 10.4529979450 region=water
O 0.7808154991 5.7886588168 2.4190174841 region=water
H 1.5418975132 5.5970474597 2.9633735143 region=water
H 0.2649331346 4.9382986570 2.3074530925 region=water
O 3.1292098263 9.8468621317 3.5876853133 region=water
H 3.5786301248 10.7365347755 3.8154900198 region=water
H 3.2563141606 9.7252397853 2.6369804442 region=water
O 4.9782776928 0.8343906317 4.8940796010 region=water
H 5.1821306990 0.1402536146 5.5350262130 region=water
H 5.1877786110 1.5875242420 5.4403529695 region=water
O 3.2891430159 8.8937086155 0.9285423206 region=water
H 2.4681968615 9.3559068442 0.6575480813 region=water
H 3.6279000841 8.5343751231 0.0706584210 region=water
O 4.4000308964 0.3750670074 1.4787140676 region=water
H 3.8810606344 10.6246957995 1.0087496445 region=water
H 4.9612841282 0.7007013894 0.7881987040 region=water
O 1.0212370765 0.2392135129 2.0988215265 region=water
H 0.9743582512 1.1008423749 2.4980199113 region=water
H 1.4954647375 10.5872611284 2.6615183995 region=water
O 10.2410289397 8.6381417803 1.7725152038 region=water
H 10.7046708368 9.0837847197 2.5204463585 region=water
H 9.4461970349 8.3793357827 2.0513562477 region=water
O 8.8547254960 9.3868869475 8.0607242679 region=water
H 8.8836362963 10.0278546088 7.3410569614 region=water
H 8.4539802745 8.6075650704 7.6370716315 region=water
O 10.1027170864 3.1860415759 10.5733804000 region=water
H 10.2257942232 3.8297111040 9.9015769430 region=water
H 10.1902080017 2.2693770770 10.1226767377 region=water
O 5.2337460446 0.1860753803 9.8066883677 region=water
H 6.1502007331 0.4608413991 9.6206501503 region=water
H 4.8714482526 10.6728862890 8.9969261480 region=water
O 10.9574813205 0.3759534989 10.0593130522 region=water
H 0.6603213599 0.4823388149 10.7808040657 region=water
H 0.5547011958 0.2966152968 9.2347836317 region=water
O 7.9584685942 10.5949551877 5.5500509382 region=water
H 7.8465545660 0.2123410377 4.8559816560 region=water
H 7.7471881504 9.7563922080 5.0841850776 region=water
O 7.4726469739 1.9706038294 8.4804944348 region=water
H 7.7766362151 1.0656478407 8.6848201062 region=water
H 7.3486780613 2.4590817378 9.3435249838 region=water
O 2.8874368558 5.7420411349 9.5332730815 region=water
H 2.1101128663 6.1746997034 9.9565808935 region=water
H 2.5346459185 5.2502278171 8.7087261127 region=water
O 7.1978008312 6.8025776176 7.1664780919 region=water
H 6.4686976875 6.5961897100 7.7388543922 region=water
H 6.7954790995 6.6081091012 6.2645009596 region=water
O 2.2072152323 2.4669281386 3.7824479899 region=water
H 1.8403619060 2.9946834570 3.0147918049 region=water
H 2.6901387081 3.1093752430 4.3450920156 region=water
O 8.0596620020 0.0720584573 10.0556233509 region=water
H 8.9638214933 0.3032470960 10.3169192392 region=water
H 8.2082346350 10.1334622429 9.6114119171 region=water
O 7.4448472300 7.4425009166 0.1740824895 region=water
H 6.5643846813 7.0434070998 0.1066959002 region=water
H 7.9196570729 7.1152203292 10.3758724933 region=water
O 0.0508049500 3.0900547305 2.1887393053 region=water
H 10.4236093770 2.8937822987 2.8429889054 region=water
H 10.5205438533 2.9087827555 1.2878696754 region=water
O 5.7931051758 6.6972668191 4.6056936580 region=water
H 5.7485354905 6.1605013992 3.7630737613 region=water
H 6.1323941290 7.5470747188 4.2746595115 region=water
O 0.6325099005 7.1900090982 0.0434059502 region=water
H 0.9978597877 6.6555793519 0.7208958829 region=water
H 0.3138054400 7.9909596587 0.5488732028 region=water
O 7.0505824114 3.8388987963 0.3168969729 region=water
H 6.5175770579 3.9133797503 1.0988532548 region=water
H 7.9159039479 3.6489192675 0.5006298130 region=water
O 5.7953328512 4.8838936651 8.9319164816 region=water
H 6.3502813815 4.4753878488 9.6982909690 region=water
H 4.9661326406 5.1177643237 9.3744733754 region=water
O 2.8194862026 5.2828216432 4.4286400864 region=water
H 2.4457811147 6.1080707932 4.7590558272 region=water
H 3.6729160052 5.5565475675 4.0641939548 region=water
O 10.5263430107 9.4950637722 4.8378272755 region=water
H 0.0248726278 10.3074084534 4.8039581078 region=water
H 9.6129121798 9.8345447310 5.1353132772 region=water
O 7.2899193491 0.0481973782 1.9734805140 region=water
H 6.3580151828 0.0574410054 2.1126975731 region=water
H 7.2625487216 10.7542923674 1.0615473931 region=water
O 2.3420746635 4.4807483801 6.9317105088 region=water
H 2.4698634168 4.7032591624 5.9204548324 region=water
H 1.3983374729 4.3670481762 7.1311948327 region=water
O 0.0065051085 7.6522242322 8.3508069356 region=water
H 10.2258284942 8.3708392051 8.2298053521 region=water
H 0.0478521940 7.5243816613 9.3286017922 region=water
O 9.0965591625 5.5285835353 8.6541663091 region=water
H 9.6933472151 6.3348879325 8.5960525458 region=water
H 8.2984598249 5.7604998867 8.0656536443 region=water
O 0.4430497246 1.1355936986 5.2501586593 region=water
H 0.6365592624 1.0326511564 6.2137263091 region=water
H 1.1187580774 1.7891028757 4.9287150027 region=water
O 7.3463205717 8.6097982935 3.5288688137 region=water
H 7.1550114418 9.3781599026 2.9612695159 region=water
H 7.4954451449 7.8578163314 2.9453605626 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0 0 0 -1
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0 0 -1 0
50 52 1.0
53 54 1.0
53 55 1.0 0 -1 0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0 0 -1 0
68 69 1.0 1 0 0
68 70 1.0 1 0 0
71 72 1.0 0 1 0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0 0 -1 0
89 90 1.0
89 91 1.0 0 0 -1
92 93 1.0 -1 0 0
92 94 1.0 -1 0 0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0 1 0 0
110 112 1.0
113 114 1.0
113 115 1.0 0 -1 0
116 117 1.0
116 118 1.0
119 120 1.0 -1 0 0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 25 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_025ps`
```ams
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_020ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 50000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_020ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 3.6389385596 8.6052134140 4.1040963333 region=glycine
C 4.5037687850 9.3997282547 5.0692049360 region=glycine
C 3.7526530451 10.2616650806 6.0692546582 region=glycine
O 4.2288249227 0.3247019784 6.4098835033 region=glycine
O 2.5699821526 9.8550701927 6.6078907391 region=glycine
H 3.8085016847 7.6401908714 3.9034613596 region=glycine
H 2.6103473395 8.6104637946 4.1758948770 region=glycine
H 5.1989076734 10.0261465879 4.4371512377 region=glycine
H 5.1137632930 8.5234576541 5.4389749356 region=glycine
H 2.4601017777 8.9811707773 6.0608296961 region=glycine
O 10.1527621817 4.0004983810 10.3107514000 region=water
H 10.6237901117 4.8146035826 10.1314893054 region=water
H 10.8110217675 3.2429249820 10.1884894277 region=water
O 6.8794845222 2.3131879150 8.7266494136 region=water
H 6.7404797744 1.3878701966 8.9961713435 region=water
H 7.1139451582 2.8544282054 9.5211747595 region=water
O 1.4812203052 2.2726959046 9.8610368071 region=water
H 2.2441650488 2.4975392890 10.4150337371 region=water
H 1.8262931364 1.4050794357 9.4864009936 region=water
O 4.5876614490 5.8553606026 3.8968307364 region=water
H 4.1727319110 4.9966794838 4.3008740994 region=water
H 4.9213154098 5.6796198092 2.9827723486 region=water
O 10.1913851346 3.5753393074 5.5602940701 region=water
H 9.8216998912 2.7194111297 5.3922395926 region=water
H 0.0523966140 3.4680705469 5.9678531688 region=water
O 7.2725206279 4.8587089755 7.1237327394 region=water
H 6.5532885506 4.2922300721 7.1198779919 region=water
H 7.3825595075 5.1360172150 6.1514655092 region=water
O 4.4590868686 2.6582923025 7.5923849302 region=water
H 5.3686331455 2.5260877247 8.0093624127 region=water
H 4.1927436393 1.7525124207 7.2580213438 region=water
O 9.2361397540 0.6839845024 5.1460773770 region=water
H 9.2224214523 10.8475711013 4.5522519098 region=water
H 8.3312238684 0.9675790429 5.1024808473 region=water
O 7.3092818059 4.6236010199 10.2700050413 region=water
H 8.2978650567 4.4931940105 10.2380814159 region=water
H 7.1155413495 4.5931912044 9.2696612823 region=water
O 7.6125375469 3.6347948291 2.5460944810 region=water
H 7.8921258896 4.3857944483 3.0642745247 region=water
H 8.2767446363 3.4565142628 1.8614107015 region=water
O 4.3130950034 0.8596270662 1.1581724542 region=water
H 4.0482560497 1.7506263648 1.2775337830 region=water
H 4.3471581503 0.6788775954 0.2511874839 region=water
O 3.7682534382 3.6424353823 5.1973491278 region=water
H 3.6262065327 3.5480427570 6.1382445667 region=water
H 2.9712414562 3.2230550417 4.8008539624 region=water
O 0.4574651234 10.6851156841 8.5841594892 region=water
H 0.7987793151 10.4676507596 9.4628453092 region=water
H 0.9276518461 10.0471157299 8.0025622969 region=water
O 6.9280630859 10.7854233827 9.8482697537 region=water
H 6.7580836036 9.8666713278 10.2627667203 region=water
H 7.7282612217 10.5496567299 9.3790527411 region=water
O 6.3446620665 2.0485381110 4.8947579942 region=water
H 6.8601276564 2.5829409997 4.2784485961 region=water
H 5.4309431922 2.4189699419 5.0511561629 region=water
O 0.9579206901 10.4383173537 3.3633168141 region=water
H 0.1887361387 9.9416126491 3.4934224178 region=water
H 1.6415023561 9.8540620614 3.5854037064 region=water
O 10.4929912073 6.0562505374 6.7153209886 region=water
H 10.8686172100 5.7670195490 7.6008383808 region=water
H 10.1685690449 5.1484282065 6.4650077785 region=water
O 5.4506228705 6.4917886364 8.2277272747 region=water
H 6.0162540506 6.3126208159 8.9938063851 region=water
H 5.8756353781 6.0829819221 7.4159871248 region=water
O 5.3990049862 4.9011416021 1.5773749251 region=water
H 5.5249569655 5.1656765856 0.6469754454 region=water
H 6.2837671368 4.4367763171 1.8511376594 region=water
O 1.8153170121 2.1187110987 3.9407456203 region=water
H 2.3836060696 2.5830187052 3.2692055165 region=water
H 1.7570322141 1.1337862038 3.7969970051 region=water
O 7.1387342507 8.5275985641 6.2958451356 region=water
H 6.6626139351 7.9332433958 6.9169815774 region=water
H 7.8678533928 8.9074220916 6.9276680906 region=water
O 0.2202997224 1.5097554687 1.2344129878 region=water
H 0.6495038076 1.4011524712 2.0876807801 region=water
H 0.8590491273 1.3762398433 0.5445058679 region=water
O 6.2588761143 10.8968445483 3.0156533408 region=water
H 6.4773630529 0.7303271530 3.5852840069 region=water
H 5.5144245984 0.2979740209 2.4418664700 region=water
O 3.2448504647 6.6193390843 9.6141906090 region=water
H 3.2879485274 6.6965511063 10.5431577871 region=water
H 4.1448549758 6.7051812919 9.2617942382 region=water
O 9.3344883046 9.3653717720 3.4759454531 region=water
H 8.7041501761 9.5915758875 2.7696794235 region=water
H 9.2647503651 8.4356888277 3.5340579697 region=water
O 3.9064147452 0.1139756792 9.4333221179 region=water
H 4.8289994047 0.2522913555 9.2080491180 region=water
H 3.5730378376 10.7798700728 8.5975267564 region=water
O 6.1762833360 8.2828610880 2.1728551074 region=water
H 6.5996346921 9.0819429701 2.6046940114 region=water
H 5.6150870821 7.9834160678 2.9119523050 region=water
O 1.4125280877 9.5807654767 0.2347376655 region=water
H 2.0157725064 8.9594615622 0.5270713627 region=water
H 1.3105519462 10.0179283719 1.0303179533 region=water
O 9.8101118451 7.7240983470 0.6095473550 region=water
H 9.8557207372 7.3611536932 1.5268052435 region=water
H 9.6173077914 8.6524118640 0.7365871677 region=water
O 2.7149542259 3.1195423392 1.4984653870 region=water
H 2.4653344397 4.0406502410 1.8418648230 region=water
H 1.8646694108 2.6423771925 1.3439400270 region=water
O 6.4883781732 7.6071111556 10.4051106589 region=water
H 7.1428328266 6.8828196453 10.5125087623 region=water
H 6.5899558985 8.0432335567 0.3200900536 region=water
O 2.9088404852 6.6616612132 1.4235128078 region=water
H 3.6272693049 6.1270548813 1.6709096295 region=water
H 2.1036393778 6.2386184435 1.7607464345 region=water
O 0.7721218060 4.7817035483 1.8527008208 region=water
H 0.1599420927 4.3483527159 1.2850593140 region=water
H 0.2016466812 5.1126977674 2.6145170165 region=water
O 9.8326355190 6.2362316749 3.2902255500 region=water
H 10.3848053817 6.5594949410 4.1105965659 region=water
H 9.0471201269 5.8750115821 3.6164743690 region=water
O 8.8775224549 10.5502668403 0.8716569514 region=water
H 8.1673479048 0.0628612555 0.5409347860 region=water
H 9.4004793222 0.2327332212 1.3012482195 region=water
O 1.4706138137 3.6063475803 7.3550848284 region=water
H 1.2720855511 3.5445234786 8.3064447024 region=water
H 2.3986743865 3.3935931478 7.3831342872 region=water
O 1.0242584864 8.1149460973 5.3341737404 region=water
H 0.4059007218 8.6400963131 4.7835762648 region=water
H 0.4902198110 7.5353187482 5.9755036545 region=water
O 7.2787450963 6.3403580835 4.5502852298 region=water
H 6.3788650598 6.2961279467 4.1053425800 region=water
H 7.1836238042 7.1636270554 5.1016945813 region=water
O 8.9514713595 10.2315725627 7.4744300747 region=water
H 9.9236875511 10.2716586392 7.7276135634 region=water
H 8.9745122404 10.6695233671 6.5565147639 region=water
O 0.4681877467 6.2636172371 9.6472753810 region=water
H 10.9157686209 6.8626156008 10.2587283399 region=water
H 1.3642472098 6.6225540081 9.6384018658 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0 0 1 0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0 1 0 0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0 0 -1 0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0 0 1 0
77 79 1.0 0 1 0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0 0 -1 0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0 0 0 1
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0 0 1 0
113 115 1.0 0 1 0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0 -1 0 0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 30 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_030ps`
```ams
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_025ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 60000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_025ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.5721479767 7.7038281768 6.0815662823 region=glycine
C 3.3148805582 9.0413399756 6.0877631348 region=glycine
C 2.8914636626 10.0890581464 5.0400782566 region=glycine
O 3.4982890333 0.0922679671 4.7992345994 region=glycine
O 1.5940621681 9.8693856405 4.5278967813 region=glycine
H 3.2165171317 6.9319959853 5.9921193889 region=glycine
H 2.1754836138 7.6101262141 7.0362530811 region=glycine
H 4.4610631969 8.8417797823 5.8780684966 region=glycine
H 3.2837241073 9.4453821611 7.1471121761 region=glycine
H 1.5755613066 8.8418847212 4.5793019921 region=glycine
O 2.2504346219 3.3001651848 0.9328335037 region=water
H 1.4321888216 2.8469701115 1.0657049067 region=water
H 2.1798008571 4.2890713862 0.8225739580 region=water
O 0.4390173875 1.9193989130 6.7039098581 region=water
H 1.2880986432 1.4035853794 6.4390999367 region=water
H 10.9504924667 1.9168909519 5.8371310205 region=water
O 1.5934256210 10.6295066222 1.6731487832 region=water
H 1.4785272162 9.7696163208 1.2285356852 region=water
H 1.5125856301 10.5704382319 2.6569307764 region=water
O 1.3293271837 6.7975145594 3.5669483326 region=water
H 0.9562700299 6.3935634711 4.3431076660 region=water
H 2.1568597302 6.3044883375 3.3592097781 region=water
O 10.5473535240 7.7777937144 5.9584221684 region=water
H 10.1163881423 6.8771812494 6.1181265386 region=water
H 0.4041135497 7.5240149322 5.6450996664 region=water
O 5.6104021548 3.2747063957 5.8334163930 region=water
H 5.7695278145 2.3980476807 6.2755996650 region=water
H 6.3314345876 3.4460128493 5.1519075913 region=water
O 10.6656711475 1.0545146540 9.5120261050 region=water
H 10.9417168831 1.0710568759 8.5758704021 region=water
H 0.5021679413 1.2266879645 9.9857345645 region=water
O 8.5282440423 2.9605455661 5.0007411242 region=water
H 8.2059028229 3.6515877292 4.3270507501 region=water
H 8.3844830726 2.0836070183 4.6326202670 region=water
O 6.6279743133 4.7685142617 3.9789966346 region=water
H 7.3119624627 4.8769866226 3.2439596886 region=water
H 5.9282763618 5.4000475414 3.8654077850 region=water
O 8.3728546106 2.5878355476 9.1770348006 region=water
H 9.2341874947 2.3341023993 9.3428394052 region=water
H 8.0289667097 1.8715950605 8.6860278014 region=water
O 5.9958973123 8.2069957157 5.2390033188 region=water
H 5.8047162729 7.3644494748 5.6219261216 region=water
H 5.4026025768 8.1985557707 4.4652943256 region=water
O 8.1677834767 5.8616459196 2.1635538080 region=water
H 7.9370304580 5.5125953450 1.2549271096 region=water
H 7.7824986092 6.7002697315 2.0660276955 region=water
O 10.5005389015 1.8902061316 1.8489923695 region=water
H 9.9821106954 1.6614217354 2.6401147094 region=water
H 0.0957805526 1.0870082402 1.8465697207 region=water
O 8.5984232249 9.0373320896 1.7260598119 region=water
H 8.7571582139 9.8341306754 1.1350856375 region=water
H 9.4167704928 8.5478429706 1.6437668719 region=water
O 6.7137284933 4.2450787937 0.1434511343 region=water
H 7.4111018682 3.7214086418 10.6182501724 region=water
H 6.0621873450 3.5663610925 0.4311626497 region=water
O 4.6716748349 5.8713989034 6.5012396940 region=water
H 4.9667100562 5.0997149564 5.9744730950 region=water
H 4.7357430203 5.5750734007 7.4012607862 region=water
O 8.9241189352 8.1231086855 8.7802349545 region=water
H 8.9468248965 8.3492549792 7.9278112443 region=water
H 9.7627070443 8.3146424597 9.2056942623 region=water
O 2.5874642576 0.9655962708 8.0975057888 region=water
H 3.3232564244 1.5128892420 8.3962507778 region=water
H 2.7823547601 0.0062826554 8.3948703459 region=water
O 5.2213549266 1.7326950308 8.4552876579 region=water
H 5.5806611033 0.8050964710 8.4462550493 region=water
H 5.3016593955 1.9109240337 9.4045190048 region=water
O 3.7517938544 5.4624205031 2.8130475886 region=water
H 3.3433987233 5.6746927133 1.9461554473 region=water
H 3.5730773736 4.5258407543 2.9161324967 region=water
O 10.6510261026 5.0059761482 4.8338289221 region=water
H 10.4848891852 4.8160486891 5.7259473336 region=water
H 10.0916505471 4.3627511095 4.3947432112 region=water
O 6.6335316664 0.9334743907 1.5928111208 region=water
H 6.8761875328 0.4536020175 0.7448332779 region=water
H 7.0834702810 0.4004062226 2.2254410311 region=water
O 5.8936115567 7.2817306415 9.4309628764 region=water
H 5.9066181849 6.3222127680 9.6069231228 region=water
H 6.8462323384 7.4962715965 9.4475689485 region=water
O 2.4785868416 5.9167029970 0.2580639835 region=water
H 2.5140024214 5.8719926576 10.2694355035 region=water
H 1.9127879661 6.6852809675 0.3922583840 region=water
O 8.5001576079 9.5221446668 5.5033549137 region=water
H 9.2012908684 8.8045380049 5.6042096302 region=water
H 7.6707251308 9.0079403997 5.3327987149 region=water
O 3.2169446926 9.2812607366 9.2300235521 region=water
H 3.8280911673 8.6691626338 9.4450614070 region=water
H 2.3551183532 8.9168947814 9.4533960782 region=water
O 8.9476376230 4.9333762497 7.3971182069 region=water
H 8.7893087741 4.2967444657 6.6960715069 region=water
H 8.6458408363 4.3648070605 8.1044210626 region=water
O 0.2566232144 9.2691823258 9.6106097399 region=water
H 0.2120587084 8.9807120549 10.5275630963 region=water
H 10.8426180203 10.2209390995 9.6377804090 region=water
O 9.4688604825 0.5545994834 3.9722481288 region=water
H 9.3523082965 10.7025232165 4.4621513633 region=water
H 10.1024485754 1.0504501684 4.5331850054 region=water
O 4.6578189047 2.3090966795 0.2228889782 region=water
H 4.0949083780 2.7994241095 0.8157775311 region=water
H 5.0607324645 1.6524201050 0.9307901331 region=water
O 6.1259316182 7.7560335160 1.1849120238 region=water
H 6.1190215208 7.5153006497 0.2466044868 region=water
H 6.8818863834 8.3531535846 1.2972603198 region=water
O 4.4425261471 8.2531899345 3.1571094301 region=water
H 5.0994445329 8.3559379432 2.3835884457 region=water
H 4.1068657204 7.3292189964 3.0866319659 region=water
O 2.7579718235 3.0065764808 4.0689698099 region=water
H 3.5124664942 3.2785364586 4.5630490829 region=water
H 2.9958139910 2.0529644020 3.9881261359 region=water
O 0.3470874762 7.9979047715 1.3479909333 region=water
H 0.2218193516 7.1634932253 0.8481622947 region=water
H 0.4485075024 7.7808910792 2.2796284913 region=water
O 8.0621850297 10.7571691865 10.5809337855 region=water
H 7.6377821489 10.6622248188 9.7284388530 region=water
H 8.7507854355 0.4023032486 10.3126249799 region=water
O 10.5523588607 4.6291729768 0.9576364955 region=water
H 10.4802867949 3.7148344790 1.0981903666 region=water
H 0.3015821368 4.8231447749 1.5529306627 region=water
O 1.7530165929 6.8464431593 8.6534649356 region=water
H 1.4278649005 5.9661064726 8.4897899650 region=water
H 1.0338215458 7.4874465478 8.6755998893 region=water
O 5.5004279319 4.5331614489 8.7747783841 region=water
H 5.0389922119 3.7097500403 8.4073691118 region=water
H 5.8873273009 4.2163715198 9.6486327113 region=water
O 6.4339381954 9.9859359553 8.2922851195 region=water
H 6.1334810888 9.8840725706 7.3927337703 region=water
H 6.6868176978 9.0905422562 8.4641241334 region=water
O 0.6401426069 4.5356146107 7.9711577105 region=water
H 10.5743460185 4.7725570823 7.9784487586 region=water
H 0.7557895187 3.6627576400 7.5908818629 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0 0 1 0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0 -1 0 0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0 1 0 0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0 1 0 0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0 1 0 0
50 51 1.0
50 52 1.0
53 54 1.0 0 0 -1
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0 0 0 -1
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0 -1 0 0
95 96 1.0 0 -1 0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0 0 1 0
116 117 1.0
116 118 1.0 1 0 0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0 -1 0 0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 35 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_035ps`
```ams
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_030ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 70000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_030ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.4670141261 9.4685379494 4.2569521686 region=glycine
C 3.1882950928 10.5129915104 4.9988016058 region=glycine
C 2.3802823042 0.6801582973 5.5705676636 region=glycine
O 2.9055069600 1.7706704616 5.6539695085 region=glycine
O 1.2207559584 0.4089266626 6.2157959000 region=glycine
H 2.9066506065 8.4946896730 4.0563097506 region=glycine
H 1.5127590033 9.3534327815 4.5747167991 region=glycine
H 4.1148458829 10.8150011310 4.4653150179 region=glycine
H 3.5734574710 10.1204917594 6.0225805723 region=glycine
H 1.1511233231 10.4001560727 6.0091294514 region=glycine
O 6.1328527388 1.6811523683 0.3947443637 region=water
H 5.4943548494 2.3483780629 0.6044511333 region=water
H 5.6559790440 0.8612558550 0.3835911705 region=water
O 1.1283738066 5.4647905065 10.2487040123 region=water
H 1.7325994202 4.9624747817 9.7508375173 region=water
H 0.3428998520 5.1088112731 9.8592546136 region=water
O 0.9448949996 2.0768330562 1.5476422792 region=water
H 0.1959858168 2.4121076623 2.1217899068 region=water
H 0.5678441948 1.4635926003 0.9440091985 region=water
O 0.6875904976 10.0194337479 2.0639721399 region=water
H 0.8861155776 9.7254803348 1.2175058988 region=water
H 1.6136758824 9.9440460324 2.4843436284 region=water
O 6.8506866107 9.1150760306 2.8407767675 region=water
H 6.8838182280 9.9688202846 3.3126581374 region=water
H 6.1414612928 9.2986154378 2.2168382798 region=water
O 5.2804362754 1.2288115003 8.5372797893 region=water
H 5.6854536793 1.1331403341 9.4057626426 region=water
H 5.7555199208 2.1031786996 8.3312763088 region=water
O 8.8532965357 0.4821726167 4.4651567252 region=water
H 9.4694212628 1.3174375609 4.3890685224 region=water
H 8.9466972656 0.1238488760 5.3696826008 region=water
O 10.5650424798 3.8024938889 5.9386210679 region=water
H 0.3349207260 3.7353842116 6.5112114041 region=water
H 10.2736861781 4.7340951625 5.7906827792 region=water
O 7.1273278520 3.4988922044 7.6591568529 region=water
H 7.1149736457 4.0066499629 6.8933953143 region=water
H 7.5215609347 2.6459936476 7.4405878834 region=water
O 9.5116508850 1.0800442690 10.1596749098 region=water
H 10.2655333416 0.5043157008 9.8631291910 region=water
H 9.3263689147 0.8431713913 0.1221625923 region=water
O 6.0071373790 0.2971669502 4.6789299496 region=water
H 6.9233413661 0.2986424530 4.7982729731 region=water
H 5.5964646598 10.9091926379 5.5326460545 region=water
O 7.5744886858 5.7178179385 9.2934162837 region=water
H 8.5361495032 5.5904958406 9.1834021360 region=water
H 7.1527175090 4.8821992419 9.0839809135 region=water
O 2.1101485245 4.7065318595 3.8397286376 region=water
H 2.9385351400 4.4399954921 3.3412150684 region=water
H 1.4710372594 4.8638387258 3.1766348394 region=water
O 3.2654431152 7.7215628688 0.6863982425 region=water
H 3.6943143490 8.5568749458 0.7916954165 region=water
H 3.9628335147 7.1479227163 0.2061109746 region=water
O 5.0181171725 3.0013951721 4.0479436747 region=water
H 4.2169346141 3.1337329781 4.6036396042 region=water
H 5.0256743296 2.0734063203 3.9400913408 region=water
O 3.7868937596 6.9653341863 4.5967302367 region=water
H 3.4912601800 7.4187426164 5.4712907792 region=water
H 3.0765687941 6.3025257653 4.3502217944 region=water
O 7.0326067936 7.3593926980 4.9189926030 region=water
H 6.1090370491 7.2841262771 5.1599092993 region=water
H 7.1107912923 7.8345603638 4.0663592630 region=water
O 0.7533404455 10.3823144248 9.7427261632 region=water
H 0.4650121764 10.3633312494 8.8125842599 region=water
H 1.6281143048 10.8260324856 9.7935765271 region=water
O 7.4992772454 0.3311486594 6.9546825404 region=water
H 6.6532692664 0.2672924706 7.3987235187 region=water
H 7.9595940823 10.4764733021 7.3432779021 region=water
O 7.5049398436 4.5234665399 5.0379397315 region=water
H 7.0684556847 5.4381120761 4.8947145303 region=water
H 6.8679260520 3.9572503921 4.6156654534 region=water
O 9.8587041110 6.3109465867 4.7109640612 region=water
H 8.8786870446 6.3810705292 4.7573683059 region=water
H 10.0254163481 6.0318177785 3.7828725320 region=water
O 5.3143973483 6.0072970761 0.1138972583 region=water
H 5.0255579673 5.3009555607 10.3880176563 region=water
H 6.1847221502 5.9816281098 10.8204338412 region=water
O 4.4207354749 4.8193741898 8.1507310476 region=water
H 4.8869367355 4.0141223720 7.8395890226 region=water
H 5.0807332919 5.4365017331 8.3421742844 region=water
O 3.9835117020 3.2739364021 1.4883230104 region=water
H 3.0761195668 2.9885308015 1.4915629239 region=water
H 4.1711116603 3.6194841387 2.3851094133 region=water
O 5.3166828453 9.5247935287 9.8705840482 region=water
H 6.2446088337 9.6020771029 9.7973146635 region=water
H 5.1327468977 9.8541118413 10.6846817993 region=water
O 4.1873438677 10.1602334992 1.8143293613 region=water
H 3.6217726229 10.0772794723 2.5549778031 region=water
H 3.8169669977 10.9349600269 1.2846401227 region=water
O 9.6447176054 3.7702774727 9.2504975887 region=water
H 8.6775706497 3.6384757669 8.9861295228 region=water
H 9.9242705582 2.8533701573 9.2537130195 region=water
O 9.2579317192 8.4747252196 1.6111985546 region=water
H 10.0748570043 9.0406796525 1.8293861691 region=water
H 8.4728972249 8.9540389543 2.0744391399 region=water
O 1.9162698279 3.1581882279 7.4602035020 region=water
H 1.9165126284 2.4606205687 6.6949768586 region=water
H 2.7968670220 3.6277978518 7.3731828406 region=water
O 8.4114825203 0.3991454359 1.5828322116 region=water
H 8.6975042203 0.5560304716 2.5190919144 region=water
H 7.6554794629 0.8486811716 1.2574784473 region=water
O 5.0047081847 9.8063546545 7.0944026875 region=water
H 4.8294041458 8.8735790759 7.3706995633 region=water
H 4.9462438706 10.3384960956 7.8748275535 region=water
O 3.5903153089 7.4227550972 7.2234764609 region=water
H 2.7902301448 7.5555544434 7.8782447984 region=water
H 3.8686305627 6.4829017091 7.3981033479 region=water
O 2.7820717394 1.6586452429 9.3915907869 region=water
H 2.2567023980 2.1360746814 8.6142552129 region=water
H 3.7681133628 1.6483541078 9.0423802594 region=water
O 8.3648308972 3.9663487737 1.4182441689 region=water
H 8.3853902235 4.4602240784 0.6051983957 region=water
H 8.1715205220 3.0622640154 1.1039848412 region=water
O 9.6540740930 9.6664302628 7.2942938317 region=water
H 10.2247931744 9.0920843135 6.7793638926 region=water
H 9.3293064006 9.0294366909 8.0132755599 region=water
O 10.7859733915 6.2390194036 1.8765813201 region=water
H 10.1574140218 6.9453317698 1.8723605098 region=water
H 0.0113414052 5.8956922900 0.9726808903 region=water
O 0.4608979749 8.2881005287 5.6934576381 region=water
H 0.8476920463 7.8414082519 6.4246610070 region=water
H 10.9116526571 7.5714527508 5.1915539115 region=water
O 8.1944663753 9.3384052457 9.9329467890 region=water
H 8.3802833450 8.7694273239 10.7016145864 region=water
H 8.2447730486 10.2405759765 10.3267451141 region=water
O 10.0176651568 2.8451320412 3.3668267442 region=water
H 10.0062180241 3.1604865196 4.3445485266 region=water
H 9.3169150692 3.3642024623 2.9065088768 region=water
O 1.3865550264 7.6417094016 8.7399321004 region=water
H 1.5452636547 8.3847241515 9.3703646450 region=water
H 1.2873547095 6.8765587664 9.4192707743 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0 0 1 0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0 0 -1 0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0 1 0 0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0 0 0 1
41 42 1.0
41 43 1.0 0 -1 0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0 0 -1 0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0 0 0 -1
74 76 1.0 0 0 -1
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0 1 0 0
119 120 1.0
119 121 1.0 -1 0 0
122 123 1.0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 40 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_040ps`
```ams
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_035ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 80000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_035ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.9467323558 9.3891863815 3.5139264636 region=glycine
C 3.7319360940 10.6547735883 3.6393365036 region=glycine
C 4.4763165504 10.7917821436 4.9551762638 region=glycine
O 5.0788557114 0.8311536595 5.1960594496 region=glycine
O 4.5352567397 9.6698846185 5.8058960970 region=glycine
H 3.5388636878 8.4858679238 3.4048626772 region=glycine
H 2.0304429993 9.3040147347 4.0111121047 region=glycine
H 3.0598831485 0.6003497455 3.4780659380 region=glycine
H 4.6033679460 10.6067142754 2.8954351903 region=glycine
H 3.9160735496 9.0570321268 5.4009821131 region=glycine
O 2.7323949466 4.8741481904 2.3861075000 region=water
H 1.9124368212 5.2440532579 2.0962377588 region=water
H 3.5353826195 5.5560556524 2.2714624632 region=water
O 1.4939729522 2.7405079271 9.0753135671 region=water
H 1.7630633923 2.8812280412 8.1146114428 region=water
H 2.1723533022 3.1353381532 9.5698467199 region=water
O 10.8334084076 6.3179508679 5.4583234553 region=water
H 9.9575700004 5.8743626957 5.1250246164 region=water
H 10.6414985641 7.2807809996 5.5284966204 region=water
O 1.4563564892 10.3623902526 0.7396701434 region=water
H 1.9979395669 9.9901805319 1.4087612084 region=water
H 1.4580729528 0.2723038875 1.0466711147 region=water
O 10.8030863228 7.2920497708 2.0461899418 region=water
H 0.1253012404 7.9175655910 2.6558347822 region=water
H 9.8480451571 7.1316802024 2.3427583245 region=water
O 5.1460997788 1.3933957642 9.6580719641 region=water
H 5.5206312223 1.8376831761 8.8627947058 region=water
H 4.7834937710 2.2297171422 10.1364227068 region=water
O 10.2275213148 1.4502575179 4.0621198280 region=water
H 9.6401765437 2.0635130536 3.5688078549 region=water
H 10.2822209381 1.7900121089 4.9507885117 region=water
O 10.4051238140 5.0020425793 8.7068099781 region=water
H 10.2163615680 6.0044706108 8.5148058997 region=water
H 10.8051698818 5.0158400993 9.6427983228 region=water
O 4.4424344026 9.1129236864 9.0894540945 region=water
H 5.1731440647 8.5014829805 9.0069967719 region=water
H 4.9518320769 9.8713378645 8.6766050066 region=water
O 2.1255075972 2.8362630533 6.1272092437 region=water
H 1.2027811459 2.8842308378 5.8885280590 region=water
H 2.3885008649 1.8830799472 5.9689535527 region=water
O 6.2828173125 0.2498211490 2.0786116608 region=water
H 7.0539563640 0.2279925382 1.5303967916 region=water
H 6.1339166918 1.1594644989 2.4907126239 region=water
O 7.4058755328 8.0366946075 8.9927260250 region=water
H 7.5224813867 8.4321587151 8.1583891584 region=water
H 8.2601319977 7.5863698713 9.1481255944 region=water
O 0.9077192005 2.1655858964 1.1534447162 region=water
H 0.4374949304 2.1085245097 0.3576723247 region=water
H 0.8683083417 3.1383951474 1.2528292546 region=water
O 3.1947644462 6.2728867190 8.4574703275 region=water
H 2.9949054853 6.5251726345 7.4716752803 region=water
H 2.6986477661 6.9362173349 9.0620116268 region=water
O 6.2649109053 6.2405157688 4.8940502142 region=water
H 6.6010534338 6.3789105358 5.8619345782 region=water
H 5.6410749976 5.5687450289 5.0396107183 region=water
O 2.9318199155 6.9290732509 5.7083719643 region=water
H 2.0043922837 6.8767887860 5.5816692600 region=water
H 3.2009220866 5.9973321205 5.7338179324 region=water
O 7.6857772173 9.2307014411 6.5542510143 region=water
H 8.3499414435 9.4085539237 5.9534407095 region=water
H 6.8690986070 9.4884063048 6.0621009853 region=water
O 10.0995152192 7.5892493350 8.9048470952 region=water
H 10.5867647440 7.9538509203 8.1072417074 region=water
H 10.7540046577 7.3971446296 9.5844232198 region=water
O 8.7161988560 10.7477619476 0.8681175514 region=water
H 8.5433768321 10.2686773273 0.0329027419 region=water
H 8.8010273793 0.7388237286 0.6730782823 region=water
O 8.8052819738 4.9009596012 4.4284606987 region=water
H 9.0794535127 4.5914823906 3.5568377501 region=water
H 8.2658484655 5.6771729899 4.2402082324 region=water
O 5.8511539544 6.0212915850 7.9746758433 region=water
H 6.3011389557 6.6311678990 8.5372007237 region=water
H 4.8767294330 6.0037511977 8.2496632541 region=water
O 4.5630051090 7.1675901500 2.5297879744 region=water
H 5.3665270258 7.4368809577 2.0663171911 region=water
H 4.9680867941 6.7891958555 3.3343214574 region=water
O 6.3673931234 2.7520912388 7.0884465246 region=water
H 6.2209483803 3.7067193413 7.0878989340 region=water
H 6.1792806920 2.2976745343 6.2583188982 region=water
O 4.9293471129 2.5363233172 2.8892902624 region=water
H 4.0769165209 2.9316913653 2.7288998327 region=water
H 4.7480212464 2.0228388691 3.6879791111 region=water
O 3.9194224936 4.0070945916 10.4819565343 region=water
H 3.2983338216 4.4217419959 0.1934522617 region=water
H 3.9014389173 4.6947024159 9.8386661144 region=water
O 1.7923629755 8.0558711478 9.9337560154 region=water
H 1.4636452936 8.5876532918 10.7000021553 region=water
H 2.5689976405 8.5613801918 9.7111263503 region=water
O 8.3139512115 2.3840880730 0.2113606250 region=water
H 7.6011526672 3.0223275434 0.0129066867 region=water
H 8.6074229900 2.0507026286 10.2684623327 region=water
O 8.4267196780 7.3926214922 3.0600661183 region=water
H 8.6783101811 8.1563569014 3.6140956170 region=water
H 7.8511959072 7.9616459907 2.4058788888 region=water
O 1.8599476874 0.2608305585 6.4927516191 region=water
H 1.3939184917 0.3045361368 7.3626169583 region=water
H 2.4007167404 10.4012466633 6.6294734662 region=water
O 6.5642745464 8.5771353374 0.9219655776 region=water
H 6.4288278861 9.4699436233 0.8119170687 region=water
H 6.6791230941 8.1834071910 0.0693289076 region=water
O 8.5718362703 0.9317703883 8.9102642075 region=water
H 9.5656272719 0.6738526128 8.9428468730 region=water
H 8.3798139298 1.2199251756 8.0482410172 region=water
O 4.0795883160 4.5583269982 4.9264095614 region=water
H 3.5091985305 3.9335030032 5.4546987013 region=water
H 3.9872068522 4.2789641148 4.0252718181 region=water
O 0.5658106146 0.2906610724 9.1443297335 region=water
H 0.8116005134 1.2426743477 8.9531892115 region=water
H 1.2421354258 10.9024972486 9.7075709870 region=water
O 6.2377949982 4.1418588541 0.7646585317 region=water
H 5.9788432236 3.7224873280 1.5795762119 region=water
H 5.4977749061 4.0211478732 0.0323403936 region=water
O 10.3521449203 3.2195098371 6.2367101534 region=water
H 10.4092077845 3.6450077981 7.1014038849 region=water
H 10.2802126154 4.0199073113 5.6832831930 region=water
O 0.3572083699 5.1335725466 0.2808417299 region=water
H 0.6631864609 5.9209295648 0.5342258164 region=water
H 10.4935816832 4.9482382482 0.8376220949 region=water
O 0.3115217951 9.5309838584 3.9237552853 region=water
H 0.3449288753 10.4252756766 3.6366408487 region=water
H 10.7193322565 9.7614739311 4.6934091923 region=water
O 8.2909817171 10.5816822049 4.1134051811 region=water
H 9.0931131917 0.1728649047 4.0322826317 region=water
H 7.7439590591 10.8631040212 3.4047573998 region=water
O 9.7037941697 3.7757215912 2.0324129436 region=water
H 8.9796791813 3.4140310125 1.3942342252 region=water
H 10.3557009340 3.0058570347 2.2095199519 region=water
O 10.9118680734 9.0446131293 6.7080266488 region=water
H 10.8397491656 9.8941670891 7.0971055584 region=water
H 0.8365462893 8.8475291635 6.7552119821 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0 0 1 0
2 9 1.0
3 4 2.0 0 1 0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0 0 1 0
23 24 1.0 1 0 0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0 0 1 0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0 0 0 1
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0 0 0 -1
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0 0 -1 0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0 0 -1 0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0 -1 0 0
119 120 1.0
119 121 1.0 -1 0 0
122 123 1.0 0 1 0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0 1 0 0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Equilibration, cumulative 45 ps
Provenance: `/home/ubuntu/work/02-equilibration_workdir/eq_045ps`
```ams
LoadSystem
File /home/ubuntu/work/02-equilibration_workdir/eq_040ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 90000
Restart /home/ubuntu/work/02-equilibration_workdir/eq_040ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type Berendsen
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 5.1028097341 7.7496697663 5.2917141543 region=glycine
C 4.8048772333 9.1814028583 4.9060392250 region=glycine
C 3.5379981355 9.9018993179 5.5096196540 region=glycine
O 3.2612843685 10.9501080879 5.0592159958 region=glycine
O 2.9515141751 9.2894941732 6.6222663159 region=glycine
H 5.5660467912 7.1809231042 4.5317382561 region=glycine
H 4.2814631350 7.3379944540 5.6924151909 region=glycine
H 4.8519786018 9.2051886972 3.7792580016 region=glycine
H 5.7666582426 9.7629576751 5.2215327763 region=glycine
H 3.3451124374 8.4791711957 6.6581942103 region=glycine
O 4.7783041050 5.7378643876 1.7879345155 region=water
H 5.4276399709 6.0880132432 2.4824673347 region=water
H 4.9613326187 4.8430753192 1.7705836259 region=water
O 1.3139492092 3.3512065067 9.3120556524 region=water
H 0.6479464707 3.5101194967 8.6257880624 region=water
H 1.4888691198 4.2701440528 9.6156078108 region=water
O 2.0454164422 8.0333720714 3.6193273929 region=water
H 2.0876913498 7.4638057466 2.7921838760 region=water
H 1.8273426974 8.9432366381 3.4349813722 region=water
O 2.6315649488 1.1715710301 1.6940249248 region=water
H 2.6753456932 0.7993466491 2.5702394733 region=water
H 2.8849184612 2.1173921388 1.9407560514 region=water
O 2.4159794115 9.8252425416 10.8524509773 region=water
H 2.2253848880 10.1465978470 9.8930938105 region=water
H 2.4206634060 10.6520886587 0.4719266963 region=water
O 2.3351532747 3.4490272141 3.4694210429 region=water
H 1.6121597254 2.7860904651 3.6108556406 region=water
H 2.9064821288 3.2669293024 4.2091461871 region=water
O 0.1434237500 2.0350333754 0.4496778241 region=water
H 0.8455126477 1.6104546165 0.9725500453 region=water
H 0.5747316581 2.7826107244 10.9656806587 region=water
O 6.7528061597 8.2099229520 10.4367531395 region=water
H 5.9876164785 8.0136006280 9.9151920231 region=water
H 6.7958767708 7.3463008766 10.8452077581 region=water
O 8.3552806373 10.3006715494 9.7975186814 region=water
H 8.7403375754 10.2728234568 8.8983211058 region=water
H 7.6462789798 9.6312931051 9.8373422578 region=water
O 8.2549038417 2.2341480373 7.8990433385 region=water
H 8.6015490185 1.3424411233 8.0592793646 region=water
H 8.7380237859 2.5603969345 7.1411309689 region=water
O 5.4110202808 9.7016329181 1.8954747792 region=water
H 5.4019207529 10.4913843122 1.3210217029 region=water
H 6.0119912049 9.0644971284 1.3819726919 region=water
O 7.5625365551 3.5781918821 10.2396987951 region=water
H 6.9435311074 2.9307415744 10.5640372454 region=water
H 7.8135191597 3.2985070025 9.3430191125 region=water
O 8.0799242395 4.2771428344 2.0361165444 region=water
H 7.8510399977 5.0734008537 2.4958596451 region=water
H 8.5787093692 4.5225101925 1.2696859144 region=water
O 9.4801730335 5.6436731375 10.7756965354 region=water
H 8.7250718732 5.0912451275 10.4084906560 region=water
H 9.7847612890 6.3703215108 10.1636207612 region=water
O 3.6913242820 3.2228011803 6.0475006230 region=water
H 3.0737471392 2.8657943656 6.6502428016 region=water
H 4.0705315113 3.9875747278 6.4863377585 region=water
O 0.0409938244 6.6362092206 4.7912972155 region=water
H 0.6323728266 7.1933438834 4.3932658360 region=water
H 10.4443295261 6.4197962445 4.0132990289 region=water
O 6.9448250574 6.7362363209 7.5045385744 region=water
H 6.3743995699 7.3439917232 6.9751475226 region=water
H 7.4858019192 6.3282520026 6.7539184621 region=water
O 8.8124164380 8.7701381842 3.5729852075 region=water
H 9.4256150078 8.1708365203 3.2419994713 region=water
H 8.6393385965 9.3807654639 2.8656938219 region=water
O 10.1656125236 10.8983022315 6.9935363874 region=water
H 10.7913149396 10.8041428986 7.7742189073 region=water
H 9.8649587511 9.9956671586 6.6328737716 region=water
O 10.8860602986 5.0995005610 7.0348912164 region=water
H 10.6889701715 4.3000432730 6.4914619432 region=water
H 0.2765420545 5.7474024397 6.4004443631 region=water
O 5.0172466575 5.1064174808 8.4807385461 region=water
H 4.7562143414 5.6641431746 9.1898183514 region=water
H 5.8759281680 5.6052146572 8.1192795929 region=water
O 9.3133268235 10.5554956447 1.3406211922 region=water
H 8.8447901038 10.3306793974 0.5402022273 region=water
H 9.6416573050 0.4178065612 1.1726673476 region=water
O 6.5671728630 2.1061405531 3.1723294924 region=water
H 6.3027681315 1.4049914530 2.5755470043 region=water
H 7.1357191051 2.7520682813 2.7513747415 region=water
O 6.9179924897 6.8129548983 3.4080827267 region=water
H 7.1160217395 6.2449311229 4.0716088510 region=water
H 7.2500438737 7.6548500740 3.7150633081 region=water
O 4.2638425209 3.6216759296 10.6734058583 region=water
H 3.4518783932 4.1222814850 10.6012714100 region=water
H 4.5905525215 3.3798681324 9.7857474774 region=water
O 1.8815430216 5.8270202214 10.5008600711 region=water
H 1.2301846928 6.4674094130 10.3998859829 region=water
H 2.5312364072 5.9744916251 9.8484543359 region=water
O 10.2506738564 6.5767209214 2.1922270185 region=water
H 10.0319918140 6.0163747782 1.4105264298 region=water
H 0.2402779045 6.5454888738 2.2710202288 region=water
O 0.4626462930 10.3234801818 3.2533116455 region=water
H 0.3035874603 10.8776551787 4.0080610538 region=water
H 10.5263466966 10.1482534878 2.9555678954 region=water
O 0.7367780693 1.5517807215 5.1533730232 region=water
H 0.1481868133 1.1009219724 5.7561045839 region=water
H 1.6157054732 1.0977227096 5.2401781555 region=water
O 4.0288829682 7.3972121389 10.4046705121 region=water
H 3.6413415988 8.2689147844 10.6417954668 region=water
H 4.2309039046 6.9811653376 0.2398736880 region=water
O 5.4631629593 1.8344539149 8.3622958278 region=water
H 6.2549985063 2.3924743294 8.2305581723 region=water
H 5.2271874574 1.4257692469 7.5357358714 region=water
O 9.4807851056 3.1258831786 4.9119210128 region=water
H 10.0230102994 2.3424225471 4.8508850348 region=water
H 9.2275382605 3.3512008800 4.0136670566 region=water
O 0.2820689819 8.0062464840 9.6878547319 region=water
H 0.7821481157 8.7677748469 9.8404581067 region=water
H 0.3058841488 7.9255809141 8.7193440848 region=water
O 1.3489396119 10.8865341728 8.6564618840 region=water
H 1.8154283896 10.5943117282 7.8458204470 region=water
H 1.7363766932 0.7452875805 8.7645674581 region=water
O 8.3261627900 5.5289042093 5.5450871266 region=water
H 9.1750950627 5.9823255017 5.5362236756 region=water
H 8.5150763152 4.5873416461 5.6771390157 region=water
O 2.0905625816 5.8740661692 2.3231295411 region=water
H 2.0894195724 5.1350967465 2.9843843597 region=water
H 3.1076096521 5.8820555123 2.0217955427 region=water
O 3.2244527175 6.4937764233 6.8191894368 region=water
H 3.7253666555 5.9435797123 7.4247875709 region=water
H 2.4510333056 5.9447083436 6.4242680463 region=water
O 6.6885200504 0.4489294273 5.5628953545 region=water
H 6.9104045196 1.1227646210 4.9526389967 region=water
H 7.0264116746 0.8888151127 6.4386791465 region=water
O 5.9745704408 1.0777394919 0.2145466917 region=water
H 6.7140712247 0.7163696680 10.6824243116 region=water
H 5.4324425148 1.4254207028 10.5089661915 region=water
O 9.9981751760 8.1510227948 6.9821390367 region=water
H 9.1392088779 7.6616941456 7.2124461231 region=water
H 10.2543315015 7.6839381750 6.1410170459 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0 0 0 1
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0 0 0 -1
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0 -1 0 0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0 1 0 0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0 0 1 0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0 1 0 0
92 93 1.0
92 94 1.0 -1 0 0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0 0 0 1
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0 0 1 0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0 0 0 -1
125 127 1.0 0 0 -1
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Production, cumulative 100 ps
Provenance: `/home/ubuntu/work/03-production_workdir/prod_100ps`
```ams
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
InitialVelocities
File /home/ubuntu/work/02-equilibration_workdir/eq_045ps/ams.rkf
Type FromFile
End
NSteps 200000
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 4.4061911919 6.6382997924 4.6818611363 region=glycine
C 2.9011537651 6.5068497391 4.6001692807 region=glycine
C 2.1844267672 6.6689424639 5.9431904526 region=glycine
O 1.0608395049 6.9931581733 5.9236623627 region=glycine
O 2.8659301808 6.2298745091 7.0450067738 region=glycine
H 4.9643151681 6.5950468929 3.8064605126 region=glycine
H 4.9093307654 5.9961781259 5.3647451961 region=glycine
H 2.6633648502 5.4772084251 4.0891965463 region=glycine
H 2.6316642921 7.3571776626 3.8755224204 region=glycine
H 3.7649636441 5.8786523529 6.7080338471 region=glycine
O 7.2248321700 1.0971813073 9.5466409094 region=water
H 6.4619604764 0.6635533108 9.1812986813 region=water
H 6.8978869139 1.9070052837 9.9087475165 region=water
O 10.2356875898 3.4526585220 0.0978747076 region=water
H 0.1427643305 3.2384931756 10.8235976375 region=water
H 10.1403807752 4.4313051429 10.9443398769 region=water
O 10.7084252191 9.6544699547 4.1862413312 region=water
H 10.7681240440 10.5088789465 3.7143472287 region=water
H 9.7181834997 9.4121245626 3.9960743735 region=water
O 10.6898422162 6.6909961589 10.4108905996 region=water
H 10.5602848583 6.9378122582 9.5146506949 region=water
H 0.5866754246 7.1130936560 10.6877440943 region=water
O 1.3662642589 0.5236663950 1.2351801097 region=water
H 2.0815404227 0.0383536250 1.5227614828 region=water
H 0.5733444170 10.9542192482 1.1661618513 region=water
O 5.8337584358 1.3338983976 6.7744035222 region=water
H 6.4388337868 1.2690403356 6.0690348136 region=water
H 5.8838357387 0.4290942861 7.1206941984 region=water
O 9.3561908371 2.7163488381 2.5101730841 region=water
H 8.3583611699 2.9615254469 2.4036883395 region=water
H 9.6969224188 2.6670464489 1.6445871982 region=water
O 6.5571299184 2.8420332696 2.1093299384 region=water
H 6.7645918262 1.9717853192 1.7841406979 region=water
H 6.5127897955 3.3952736268 1.2854016687 region=water
O 8.2825622033 7.4200473000 5.7895609281 region=water
H 8.9699431126 7.4465287230 6.4797779371 region=water
H 7.5388838102 7.9974687846 6.2123756184 region=water
O 1.2760834370 2.8662278413 5.9950004260 region=water
H 0.8791436997 2.6421916973 5.1190250191 region=water
H 2.2203608259 3.2273186660 5.8269558867 region=water
O 4.9817811109 9.8735233434 4.3201879608 region=water
H 4.0646126402 9.9627307351 4.6951367213 region=water
H 5.4051931988 10.7763014896 4.3286630705 region=water
O 5.0253692900 10.3723015586 8.8476434622 region=water
H 4.1523780437 10.4871323204 8.5426827511 region=water
H 5.4644606694 9.7300706932 8.2476402135 region=water
O 6.3772433821 6.2256730393 9.7246478566 region=water
H 7.0943240212 5.6193372192 9.9190669301 region=water
H 6.2213799606 6.2131343374 8.7526169876 region=water
O 9.5210862586 10.1649727241 0.6905795289 region=water
H 8.6626678149 9.9999331237 0.3139096059 region=water
H 9.4888147109 9.6418614053 1.4864686579 region=water
O 9.4530154638 4.1422534846 6.0042492975 region=water
H 9.4595599096 4.8012742040 5.3538427560 region=water
H 10.3422327925 3.8492400991 6.0480774337 region=water
O 1.5724269709 8.4472294058 2.6357690841 region=water
H 1.4592611371 8.3942479483 1.6882433985 region=water
H 0.7056592888 8.7511681101 2.9698797133 region=water
O 8.4200962649 8.6345449606 3.2539641877 region=water
H 8.5914210775 7.9104426865 2.4923653209 region=water
H 7.9241053529 8.1588951697 3.9264344928 region=water
O 6.5472565036 0.1394831269 1.7225998587 region=water
H 6.1741097992 10.8400249490 2.5696985199 region=water
H 6.8273496798 10.3689908163 1.1261102967 region=water
O 2.6434970719 9.8337524848 7.6922235261 region=water
H 2.2076789251 10.1017797523 6.8929110680 region=water
H 1.8443403373 9.5032563578 8.2193255372 region=water
O 3.8669323998 3.0655484360 5.5866514863 region=water
H 4.4190829766 2.6375145241 6.2836401159 region=water
H 3.9101005763 2.5062178496 4.7980938509 region=water
O 5.4722398514 3.2342651971 10.5771267588 region=water
H 4.5238474085 3.3447374291 10.8725107960 region=water
H 5.7064429567 4.2311995110 10.5734046355 region=water
O 7.5533121647 0.0651571925 4.7584941205 region=water
H 8.4960783961 10.9676233474 4.8647829348 region=water
H 7.2428042440 10.5107913824 4.0705273364 region=water
O 4.1174946225 1.4390880672 3.2118982318 region=water
H 5.0306156544 1.6704604136 3.0223966865 region=water
H 4.1873389593 0.5289169004 2.9671666464 region=water
O 6.0107602852 6.2954893781 2.2540993784 region=water
H 6.8364555114 6.3589172875 1.8341548531 region=water
H 5.4049979972 6.2625655543 1.4780024343 region=water
O 1.8139243293 1.5481575667 8.9251930696 region=water
H 1.5537441553 0.6157901931 8.6666546060 region=water
H 1.8055074367 1.9242936379 7.9857564249 region=water
O 3.8526105160 6.0034374235 10.8091282767 region=water
H 4.7833367307 5.9149530586 10.4004189476 region=water
H 3.1783771293 5.3782527996 10.4747606186 region=water
O 8.8152337242 6.5227579426 1.3549909026 region=water
H 9.5742983632 6.6967114576 0.6183862375 region=water
H 9.2750000160 6.3636561546 2.2618434444 region=water
O 2.3105235603 10.4699940571 5.1961802402 region=water
H 1.8223280964 9.8488406783 4.6023933826 region=water
H 1.8996056310 0.3162590353 4.9787726168 region=water
O 2.4147730888 3.3309672894 0.2179026166 region=water
H 2.2066600743 2.9619296425 10.3016611177 region=water
H 2.4656612427 2.5670787604 0.7820299141 region=water
O 2.0714629997 8.0701191564 10.7501900204 region=water
H 2.5616826958 8.9372724156 10.8739492235 region=water
H 2.6958305479 7.3771735155 10.6320089398 region=water
O 7.0053511196 8.9047218716 10.7162309306 region=water
H 6.4833980559 9.1629150299 9.8847620248 region=water
H 7.0487810076 7.8962460834 10.6285045160 region=water
O 0.6077873213 1.7328457566 3.5968861478 region=water
H 10.8018920722 2.3253091583 3.5055684221 region=water
H 0.9021022073 1.3621553974 2.7079785054 region=water
O 10.1392144586 7.4850616289 7.6713968975 region=water
H 10.5525802597 8.2606645586 8.0848313100 region=water
H 10.8076316543 7.0746664260 6.9601202768 region=water
O 10.8420467466 9.8932866562 8.9511787679 region=water
H 10.4277720633 10.4108767633 8.3103517365 region=water
H 10.2908746330 9.8529879084 9.8160096177 region=water
O 9.9309364562 6.0623718415 3.8979818559 region=water
H 9.4296031178 6.7537456890 4.2736328627 region=water
H 10.8753257794 6.2878414385 3.8872421776 region=water
O 2.1908837623 4.4990860759 2.4816901365 region=water
H 2.3542708980 4.5767039470 1.4976344283 region=water
H 2.1469210043 3.5970155148 2.7112959446 region=water
O 5.9109944360 5.5373372647 6.7952995710 region=water
H 5.8849933137 4.6092591807 6.7444276850 region=water
H 6.7709584141 5.7864076275 6.5609136066 region=water
O 6.1150596865 8.7462044579 6.9006673539 region=water
H 5.7096698078 9.2276049907 6.1214861302 region=water
H 5.8401049204 7.8307632477 6.6637554054 region=water
O 3.5203795919 10.3396912488 0.1518181652 region=water
H 4.2386238158 10.5727932838 10.4922441630 region=water
H 2.8187299231 10.9181701478 10.8755554718 region=water
O 9.1777802430 0.5183149149 7.1102577778 region=water
H 8.5285110835 0.5660986913 6.4805242314 region=water
H 8.6707967387 0.6064705859 7.8993773507 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0 1 0 -1
14 16 1.0 0 0 -1
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0 1 0 0
23 24 1.0
23 25 1.0 0 -1 0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0 0 -1 0
62 64 1.0 0 -1 0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0 0 -1 0
74 76 1.0 0 -1 0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0 0 1 0
95 96 1.0 0 0 -1
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0 -1 0 0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0 0 0 -1
125 127 1.0 0 0 -1
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Production, cumulative 150 ps
Provenance: `/home/ubuntu/work/03-production_workdir/prod_0150ps`
```ams
LoadSystem
File /home/ubuntu/work/03-production_workdir/prod_100ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 300000
Restart /home/ubuntu/work/03-production_workdir/prod_100ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 2.8760759835 0.1088542459 7.0275643728 region=glycine
C 1.5391470307 10.6667730325 7.6106780759 region=glycine
C 0.9576985468 9.3661865042 7.0573136225 region=glycine
O 0.2191137535 8.7216094609 7.7006474106 region=glycine
O 1.3448910813 8.9938006531 5.7857149476 region=glycine
H 2.8029164563 0.4232209132 6.0546080143 region=glycine
H 3.2451149907 0.8759456645 7.5630947758 region=glycine
H 0.8004806987 0.5198694477 7.4670514552 region=glycine
H 1.5860833343 10.3089351768 8.6843151431 region=glycine
H 1.8306634705 9.7987908426 5.4724390061 region=glycine
O 3.0481751759 8.8863314294 2.5194162069 region=water
H 2.4833756051 8.5284269305 1.7493224642 region=water
H 3.8497629136 9.2371958370 2.0515990287 region=water
O 7.3661550940 9.0430684653 7.5756013870 region=water
H 7.7763787738 8.2395857800 7.2165762260 region=water
H 6.5095254906 9.1975398441 7.1368686109 region=water
O 10.2256409807 5.2478831500 5.0677714071 region=water
H 9.9516298942 5.7368397021 5.8970307827 region=water
H 0.1936605440 5.5119353361 4.8469727557 region=water
O 5.5314467251 5.4014214933 0.6050413270 region=water
H 4.8973473295 5.2235645104 1.3970446879 region=water
H 6.2630636279 5.8344128445 0.9373951351 region=water
O 4.1183765496 8.6692738681 8.6876499588 region=water
H 3.5053730239 9.2233684633 8.1379614308 region=water
H 4.9475176350 8.6847336879 8.1478807521 region=water
O 8.5474308582 5.1230802852 9.8126331947 region=water
H 7.9251368519 4.8229765980 10.4593513806 region=water
H 9.3655630457 4.7068977735 10.1807203186 region=water
O 9.8981993222 9.3993222083 10.1693046932 region=water
H 9.1393583229 9.9324842000 9.8537754428 region=water
H 10.4731904759 9.3325209186 9.4156795065 region=water
O 7.7062051012 8.1609197755 0.6881788892 region=water
H 8.5731788640 8.1842557740 0.1856145638 region=water
H 7.8237646902 7.4345858221 1.2634700422 region=water
O 5.9291869331 1.8937868620 10.8080153022 region=water
H 6.6444777550 2.5106424968 10.9434006386 region=water
H 5.7649531725 1.5884883062 0.7591332379 region=water
O 9.9783372166 2.5718925701 10.0097220914 region=water
H 9.6076868811 1.9214028859 9.4230559232 region=water
H 10.7295148640 2.1827125121 10.3975198690 region=water
O 8.3055113300 7.5121146321 5.3815007077 region=water
H 7.5495245742 7.6586137164 4.7706038842 region=water
H 8.8938464661 6.8940142615 4.9138865076 region=water
O 10.8148876016 9.6787844126 2.1234909744 region=water
H 10.8031156897 9.2993068930 1.1867839515 region=water
H 0.3980908653 10.4102696124 1.9976215060 region=water
O 8.4498358194 0.5601354506 8.3802668725 region=water
H 8.1844324793 10.6248214190 8.1495877267 region=water
H 7.6326052837 1.0700253349 8.2656836671 region=water
O 7.6300083337 5.2681715423 6.7467560923 region=water
H 8.3175379590 5.4274951291 7.3999553665 region=water
H 7.5861541720 6.0138329243 6.1481097814 region=water
O 5.0449193020 9.6241704318 0.9229044858 region=water
H 5.8578826749 9.1371130516 0.5824697880 region=water
H 4.6131141414 10.0273382579 0.1747432349 region=water
O 6.3763991972 2.3195749362 6.3188296386 region=water
H 6.6385024200 3.2479449458 6.3314834109 region=water
H 7.0570380850 2.0795481726 5.6900093624 region=water
O 4.4404943489 5.2652018523 3.2707679502 region=water
H 4.7371821385 6.1894994585 3.5645931310 region=water
H 3.5913440623 5.1492129974 3.7340580244 region=water
O 0.4747123905 6.1613861583 1.0577414204 region=water
H 0.8435958927 5.7238858965 0.3015232018 region=water
H 0.9680223677 7.0619410114 1.1618390926 region=water
O 10.8197636804 2.8409422143 3.2125763435 region=water
H 10.5569894619 3.4692415674 3.8813323798 region=water
H 10.0503225645 2.2028257659 3.1465235366 region=water
O 2.4490308554 0.1657031760 4.2751894719 region=water
H 2.4038625125 10.4524579311 3.6190825721 region=water
H 2.8206373973 0.9087657848 3.8062592285 region=water
O 5.6875181376 7.4880763125 3.7554055362 region=water
H 5.2279170868 7.9185030139 2.9788576074 region=water
H 5.2476243097 7.9363914491 4.5978528378 region=water
O 5.5793003127 2.6171007930 2.1423811926 region=water
H 4.6221893666 2.8110227462 2.0541654227 region=water
H 5.9796487944 3.4325976386 1.7329367193 region=water
O 5.4242818006 9.7307800835 5.5915274082 region=water
H 4.6488785599 10.1833039781 5.9547238467 region=water
H 5.7405658126 10.4054832231 4.9165416719 region=water
O 1.9725449923 6.0612397903 4.4786526099 region=water
H 2.2747039325 5.4251903749 5.1488652671 region=water
H 2.0601184872 6.9197378537 4.9658161518 region=water
O 9.6093507913 1.8919691605 6.3638223006 region=water
H 9.0285344348 1.6875129399 7.1356807503 region=water
H 9.4069520269 2.8488353846 6.1430732221 region=water
O 2.8092743952 2.6328170642 2.8998358314 region=water
H 1.9339214958 2.6811706150 3.2793514048 region=water
H 3.2440378322 3.4818659272 3.2240999088 region=water
O 8.7208502055 6.0720205465 2.2969285977 region=water
H 9.6313282926 6.2920993242 2.0008340377 region=water
H 8.6066099540 5.1990470374 1.8037150063 region=water
O 9.0971247021 0.7184539376 2.5443912823 region=water
H 8.2743102168 0.4099314830 2.9051156300 region=water
H 9.6940265765 10.8998932734 2.4837721672 region=water
O 0.8841929838 1.3220572198 0.8644206388 region=water
H 0.1546613914 1.2513087235 1.5137752105 region=water
H 1.6177024427 1.5759131621 1.3580510158 region=water
O 2.5818440159 0.2589946421 10.0817016527 region=water
H 2.0727201701 0.9584868508 10.5393505561 region=water
H 3.1078528928 0.7268578700 9.4803136045 region=water
O 4.7439178812 5.0822041567 7.0006815515 region=water
H 4.5902526312 5.0741890541 7.8976517311 region=water
H 5.7299669079 4.8331924712 6.9046766575 region=water
O 4.4462894505 2.0455249819 8.3891853504 region=water
H 5.1599120652 2.2169861343 8.9692298153 region=water
H 4.8093776551 1.9954960384 7.5190226781 region=water
O 2.5528975998 3.7743138808 6.0889334061 region=water
H 2.0195413178 3.4431034012 6.7348860573 region=water
H 3.2506926349 4.3156831114 6.5769691989 region=water
O 3.5767942589 5.9188977566 9.5854699420 region=water
H 4.2725207960 5.5593385317 10.2784700284 region=water
H 3.9280086918 6.8241211310 9.3593886050 region=water
O 0.7699183977 2.5684603728 7.7745894471 region=water
H 0.0589476973 2.4523581775 7.0859921480 region=water
H 0.3718767702 3.0769430906 8.4970752789 region=water
O 1.0014883500 5.0517268839 9.4932983740 region=water
H 0.6162702652 5.4332021328 8.7203007287 region=water
H 2.0032309813 5.1324772313 9.4367674504 region=water
O 8.8329867845 3.6285803657 1.1583569792 region=water
H 9.5389785598 3.3087548216 0.6809147881 region=water
H 8.8726017085 3.1594043520 1.9928126299 region=water
O 10.2892997987 6.2072044528 7.6630550281 region=water
H 9.8158247117 6.1639267796 8.5053112484 region=water
H 10.3587102998 7.2182333763 7.5112942061 region=water
O 6.3932485764 10.9576461742 3.2295814729 region=water
H 6.0791018069 0.9333066271 3.2315466262 region=water
H 5.9052154973 10.5972671349 2.5009584608 region=water
O 1.9387052566 8.3153099765 0.0298559911 region=water
H 2.5134273811 8.9723787488 10.6242484666 region=water
H 1.4195442119 8.0299529447 10.2725186316 region=water
End
BondOrders
1 2 1.0 0 -1 0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0 0 1 0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0 1 0 0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0 0 0 1
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0 1 0 0
47 48 1.0 0 -1 0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0 0 -1 0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0 0 -1 0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0
122 124 1.0
125 126 1.0 0 1 0
125 127 1.0
128 129 1.0 0 0 -1
128 130 1.0 0 0 -1
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Production, cumulative 200 ps
Provenance: `/home/ubuntu/work/03-production_workdir/prod_0200ps`
```ams
LoadSystem
File /home/ubuntu/work/03-production_workdir/prod_0150ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 400000
Restart /home/ubuntu/work/03-production_workdir/prod_0150ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 7.6733102340 3.0323997704 2.8648505490 region=glycine
C 7.0133282354 1.9267093435 3.6564610646 region=glycine
C 5.4739545738 1.9558795372 3.5192272576 region=glycine
O 4.7584926420 1.6138011915 4.3737334821 region=glycine
O 5.0174998901 2.2624507612 2.2748194725 region=glycine
H 8.7333622402 3.1496647204 2.9890009493 region=glycine
H 7.2942699050 3.9754610684 3.1716890077 region=glycine
H 7.2748282344 1.9569120128 4.7458051320 region=glycine
H 7.5091680205 1.0284867421 3.2748171060 region=glycine
H 5.8477206826 2.6122181613 1.8266907808 region=glycine
O 8.6904224549 2.1365140083 0.0562170731 region=water
H 8.3894814100 2.3554554430 0.9381929568 region=water
H 9.3986170702 1.5400225910 0.1995530990 region=water
O 3.1011023315 6.2982014048 8.5578098731 region=water
H 2.4719895117 5.6348886503 8.7290098391 region=water
H 2.6138519732 7.0963551964 8.7571652715 region=water
O 2.6662528286 9.1533885595 7.5642770901 region=water
H 3.3001192520 9.9243025758 7.4462029800 region=water
H 2.2589641642 9.0403705174 6.7488832696 region=water
O 10.5454616936 5.9742200758 9.6599334126 region=water
H 10.5533524663 5.4887287063 8.8334743156 region=water
H 10.7500145017 5.2947195662 10.3221256765 region=water
O 1.9674224049 8.2838275759 4.7320959573 region=water
H 1.7840641166 9.2314148358 4.9019782302 region=water
H 1.0989494106 7.8185147267 4.7897059070 region=water
O 9.2607260001 8.3855085304 1.3077148015 region=water
H 10.1590248506 8.8041353583 1.0993561978 region=water
H 9.1697777250 7.7186154378 0.6168519112 region=water
O 7.0754881203 0.2951040678 9.7975225389 region=water
H 6.7050194303 10.4991319159 10.2727027927 region=water
H 7.6482078579 0.8451768072 10.3510979072 region=water
O 4.7821092833 9.2161915417 9.9856840683 region=water
H 5.0012786398 9.5526485184 9.1576013494 region=water
H 5.5424355445 8.5750821434 10.1701735468 region=water
O 8.4616561596 5.4688585064 6.2250076603 region=water
H 9.4071221016 5.3180807114 6.1448444013 region=water
H 8.2097819435 5.7902278021 5.3550925707 region=water
O 2.2074309860 4.6618374747 5.0447359049 region=water
H 2.0511768545 3.8967565987 4.3970051685 region=water
H 3.1169269668 4.5004474120 5.4854669698 region=water
O 6.5181597270 9.5260996255 4.5511214134 region=water
H 7.1943199583 8.8090087224 4.6062461256 region=water
H 6.3273887413 9.7374434576 5.4789972665 region=water
O 6.6999050850 7.4325952111 7.8149437485 region=water
H 6.9283327464 6.9315294362 7.0748421029 region=water
H 7.5281660669 7.3466291864 8.4301992671 region=water
O 9.8881810738 1.1415978251 7.4770909431 region=water
H 9.7567827194 1.0602253384 8.4911923757 region=water
H 9.4300858829 1.8837855830 7.0548109830 region=water
O 10.4550818726 0.0198950271 9.7629726986 region=water
H 10.4912442238 10.4271819011 9.0212498248 region=water
H 10.7357699795 10.3545238426 10.3984883862 region=water
O 3.8915485700 9.9739264293 2.3417273877 region=water
H 4.3243571856 10.4941437694 2.9507447299 region=water
H 4.3236439568 9.0655617460 2.2055392982 region=water
O 7.4664530809 10.4419045025 7.2123395613 region=water
H 7.3848099321 10.5330092210 8.1832412452 region=water
H 7.8202660911 0.3253430989 6.9173404380 region=water
O 8.1585234935 7.1780838141 9.8680907145 region=water
H 9.1201341126 6.9346658921 9.8162409574 region=water
H 7.6972006762 6.2962496119 10.0316674847 region=water
O 4.8092813462 10.7888927845 7.2069560823 region=water
H 5.7130873226 10.3738197733 7.1140019775 region=water
H 4.7124591818 0.3971811858 6.4327231698 region=water
O 4.5977097188 7.6763749560 3.5950514738 region=water
H 3.7937649176 7.6279211083 4.1335557502 region=water
H 5.0092624005 8.4809180053 4.0117957465 region=water
O 10.2676267850 8.9196139132 7.6129235729 region=water
H 10.7761643459 9.0999740541 6.8613912501 region=water
H 9.6547648702 9.7227773700 7.3652735896 region=water
O 1.2156716693 9.8863449172 1.2009283581 region=water
H 1.3082683228 9.2328151636 0.4929932922 region=water
H 2.1003283350 9.9847872829 1.5881571471 region=water
O 4.4667176397 6.1360076974 0.0435714892 region=water
H 5.3421141132 5.7740921330 10.9617508014 region=water
H 4.3858833261 6.6625694237 10.2409770113 region=water
O 10.3508900792 2.8373314906 3.8081866633 region=water
H 9.7978235071 2.0562334019 3.6129791487 region=water
H 0.1783512277 2.8732809983 3.3032236739 region=water
O 5.3666815357 2.4274001622 8.3684310309 region=water
H 5.8291569850 1.8572047631 9.0200406728 region=water
H 4.7084697255 1.7433759111 8.0536572515 region=water
O 0.3982755028 4.8816993422 0.7811310816 region=water
H 1.1704115696 5.4787748214 0.9669909469 region=water
H 0.7620080801 4.0879609925 0.3703447848 region=water
O 9.1013561310 8.2977860075 4.0459359105 region=water
H 9.0681498631 8.3225859199 3.1081641632 region=water
H 9.4134209911 7.3481390311 4.2709957484 region=water
O 2.8637052883 3.7673658431 9.5741374944 region=water
H 3.7313588580 3.3795825617 9.3731820989 region=water
H 2.3404376200 3.0701816067 10.0862177802 region=water
O 7.8205543702 2.8637611888 6.6554726883 region=water
H 7.1289208396 2.6617949238 7.3386095611 region=water
H 7.7555513084 3.8476364125 6.5704790597 region=water
O 9.1814776862 0.2164036739 3.1982932778 region=water
H 8.9903262516 10.4319582622 3.7531838068 region=water
H 9.0665043749 10.7972794705 2.3414370601 region=water
O 6.6843978695 5.7004727365 3.9516030370 region=water
H 6.2465077078 6.5431308712 4.0045993533 region=water
H 6.0367151105 5.2944695675 4.5976314549 region=water
O 6.1077714730 8.1428808198 1.0780515346 region=water
H 6.6818317282 7.5383454108 0.6742626773 region=water
H 5.3984063441 7.5227217398 1.4452729134 region=water
O 4.6287572100 4.6489590649 6.3846742983 region=water
H 4.2571759390 4.9649949624 7.2293353660 region=water
H 4.7852149562 3.7468928936 6.5191001186 region=water
O 2.7283318816 5.9374781983 2.3357862169 region=water
H 3.2959230735 5.9132142901 3.0950985176 region=water
H 3.2357088364 6.0070078986 1.5891149504 region=water
O 1.1687869725 8.0862685068 10.0843390231 region=water
H 1.7506921858 8.5074168173 9.4389199336 region=water
H 0.6272747665 7.5716593287 9.5405965202 region=water
O 0.7528567190 10.8607031747 5.6905181944 region=water
H 0.1149038681 0.1285316063 6.3350174484 region=water
H 0.8882240694 0.6792269546 5.2301135919 region=water
O 1.9902991226 2.7255169983 2.7987054082 region=water
H 2.7464992096 2.3272294401 3.1918093128 region=water
H 2.2735476682 2.5657809741 1.8462571674 region=water
O 6.9504003463 4.5905089091 10.3518570021 region=water
H 6.2743554490 4.2035182813 9.9017047301 region=water
H 7.6432113421 3.9106586342 10.4949561057 region=water
O 10.7568885511 5.8854202635 4.4003292518 region=water
H 0.6919466891 5.7867428808 4.5998715285 region=water
H 10.6134203750 4.9676611118 4.0970324233 region=water
O 0.1144360744 4.4155946649 7.5000697349 region=water
H 10.8148935280 4.5742484635 6.5458105086 region=water
H 1.0963866209 4.4559611465 7.4856516645 region=water
O 1.4294842155 1.7949922065 0.0224753923 region=water
H 0.4955894756 1.7123513471 10.6187867222 region=water
H 1.7118710704 0.8634343532 0.1327340352 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0 0 -1 0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0 0 -1 0
50 52 1.0 0 -1 0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0 0 1 0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0 0 1 0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0 0 0 -1
74 76 1.0 0 0 -1
77 78 1.0
77 79 1.0 1 0 0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0 0 -1 0
95 97 1.0 0 -1 0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0 0 1 0
113 115 1.0 0 1 0
116 117 1.0
116 118 1.0
119 120 1.0
119 121 1.0
122 123 1.0 1 0 0
122 124 1.0
125 126 1.0 -1 0 0
125 127 1.0
128 129 1.0 0 0 -1
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Production, cumulative 250 ps
Provenance: `/home/ubuntu/work/03-production_workdir/prod_0250ps`
```ams
LoadSystem
File /home/ubuntu/work/03-production_workdir/prod_0200ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 500000
Restart /home/ubuntu/work/03-production_workdir/prod_0200ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 5.1814486621 7.7899107641 1.2916261363 region=glycine
C 5.7663986049 9.1465799451 1.6173863138 region=glycine
C 5.9997307297 9.3562208147 3.1243045402 region=glycine
O 6.7976029715 10.2031794327 3.4781100739 region=glycine
O 5.2628976500 8.6602437106 4.0674310133 region=glycine
H 5.8908799659 7.0143861416 1.4091370646 region=glycine
H 4.9632922706 7.7490023704 0.2270464388 region=glycine
H 5.2105742736 9.9798842431 1.1348000940 region=glycine
H 6.8983487669 9.3266108857 1.2160343301 region=glycine
H 4.7772627981 8.0126984349 3.5034547304 region=glycine
O 10.5413001698 6.4868555110 5.7312899233 region=water
H 9.9415023794 6.6956059593 4.9453289355 region=water
H 9.8854623807 5.9965895562 6.2377557177 region=water
O 10.2649469237 4.9174262593 10.8411759354 region=water
H 10.3850511733 5.6029582756 10.2056181684 region=water
H 10.4661651067 5.3052763303 0.7595057213 region=water
O 6.1089864235 5.4735098329 6.2797572534 region=water
H 5.3859389947 5.2412971728 6.8190698326 region=water
H 6.9367652287 5.1098116072 6.7241150688 region=water
O 3.6726930397 2.5245875692 5.9479599501 region=water
H 3.7512727648 3.2823333035 6.5724652026 region=water
H 3.2809933799 1.7003823874 6.3833094575 region=water
O 6.9692605648 2.3675822630 0.3645887283 region=water
H 7.7311984884 1.7615344236 0.4498881839 region=water
H 6.8541967840 2.6579362711 1.2481247681 region=water
O 4.9068625462 0.2305660312 10.6487259302 region=water
H 4.3495308758 0.2103644183 9.8560011341 region=water
H 5.3352788077 1.1882064578 10.6824964433 region=water
O 8.9299600908 4.1766445912 7.1178493869 region=water
H 9.0258657475 4.0616197871 6.1198677321 region=water
H 8.8992049824 3.2758848335 7.4694566808 region=water
O 10.5056184166 2.1632024389 3.1221210562 region=water
H 10.2268853438 1.4254657386 3.6799054174 region=water
H 0.4352082598 2.5001696205 3.5116761135 region=water
O 6.1959715133 9.5903390314 8.2002837496 region=water
H 6.1128604011 10.5525157689 8.3294575163 region=water
H 6.2485979738 9.5710954661 7.2006306707 region=water
O 0.4231819960 9.2605825647 6.4890964122 region=water
H 0.2716499664 8.3464681013 6.2835783044 region=water
H 10.6003070587 9.4630885347 7.0182168566 region=water
O 2.1244873979 8.0532759821 2.5208939672 region=water
H 3.0108613718 8.2357675910 2.4021365637 region=water
H 2.0653352120 7.5262731070 3.2999575605 region=water
O 10.0787378692 1.5745679394 0.2152010203 region=water
H 10.5378019411 1.5244051783 1.0932715025 region=water
H 10.1671370008 2.5382020189 0.0749806815 region=water
O 1.7408638182 10.9235777120 10.2115428408 region=water
H 0.9220103980 0.1111742504 10.6357216528 region=water
H 2.3299225528 10.8926961657 0.0066802392 region=water
O 8.9808251370 7.5040213528 3.3316883562 region=water
H 8.0779632029 7.7793441125 3.1559812125 region=water
H 9.4148442830 8.3635103182 3.1248683312 region=water
O 5.0620023012 7.4993009248 9.3977137782 region=water
H 5.8065413909 6.8329289457 9.1502533177 region=water
H 5.3059551163 8.2943726801 8.9006153819 region=water
O 1.1102969113 5.6419686656 1.5677007642 region=water
H 1.9279581920 5.1305378497 1.3428337802 region=water
H 1.3933213274 6.4835196694 1.9384268939 region=water
O 5.0710662157 5.8596910493 3.7630633570 region=water
H 4.1470222835 5.7971839671 4.0377295474 region=water
H 5.5774422587 6.1036912276 4.6002129763 region=water
O 8.3311959570 10.1160644993 0.2612260809 region=water
H 8.9094013540 9.6539589908 0.9245573746 region=water
H 8.7957714424 0.0441601883 0.1574831532 region=water
O 9.5605660241 1.7474712454 8.3402686519 region=water
H 9.4205604843 0.7900068655 8.2790143916 region=water
H 9.9891952742 1.8620353799 9.2139520357 region=water
O 3.8720606165 4.2066225566 1.2110568819 region=water
H 4.7929352269 4.3798716889 1.5751218067 region=water
H 3.6087900726 3.3260244874 1.5606878404 region=water
O 1.0309374101 4.2933240614 8.2595878528 region=water
H 0.3639996329 4.1495095802 7.5327514464 region=water
H 0.4301262254 4.1450698472 8.9832660035 region=water
O 8.9810664498 4.1791909024 3.9131240493 region=water
H 9.1225279360 5.1189853195 3.7488012015 region=water
H 9.7735704742 3.6559490020 3.5904360802 region=water
O 4.7296157335 3.0232779565 9.9187118490 region=water
H 4.2974196087 3.6581615545 10.4819000275 region=water
H 5.7249115784 3.0021165066 10.1707972040 region=water
O 1.9319906164 7.7530889116 10.1524119602 region=water
H 1.7169095616 8.3647764151 10.8520549905 region=water
H 2.9493241850 7.7656737453 10.1148832336 region=water
O 6.5379506657 1.2080484749 7.8976366312 region=water
H 5.9983555517 1.6671968788 8.5412308727 region=water
H 7.4370214647 1.2153744805 8.2921131870 region=water
O 7.5658296656 5.7185629590 9.0969117888 region=water
H 7.9868173776 5.2898084038 8.3203711130 region=water
H 8.3510894565 6.2357334849 9.4099991025 region=water
O 2.1930045926 0.4289629048 7.1323847741 region=water
H 1.2380001715 0.1559647917 7.0086930738 region=water
H 2.3246918094 0.1623653454 8.1013551857 region=water
O 0.4698956501 10.9204665214 4.3225890458 region=water
H 0.6195426034 10.3444943596 5.1527536303 region=water
H 1.3243259284 10.9218177896 3.9518022047 region=water
O 10.2027433455 6.9605035216 8.7760945370 region=water
H 0.0583505249 7.2857133620 9.0975282639 region=water
H 10.4985288656 6.7291435519 7.8772187958 region=water
O 6.5897812256 5.3683341946 0.9456422810 region=water
H 6.7526596141 4.3970596989 1.1584879824 region=water
H 6.6558245104 5.4158586245 10.9603720650 region=water
O 2.4545287867 7.0376975408 5.1348540331 region=water
H 2.9601086960 7.6367612550 5.7182782382 region=water
H 1.5452933291 6.9784235691 5.4853610999 region=water
O 2.0716543961 3.0899480867 3.7231134269 region=water
H 2.7855503767 3.3356645098 3.0932251170 region=water
H 2.6940022326 2.9688541383 4.5618917337 region=water
O 6.2166313819 3.3928511003 3.5417637690 region=water
H 5.8685139310 4.2064711629 3.8936775771 region=water
H 7.2015519175 3.4339202846 3.4613169512 region=water
O 3.8120494709 8.9452137440 6.4453935590 region=water
H 4.3621666303 9.2597945490 5.7771741490 region=water
H 3.0412202721 9.5688215718 6.4752081339 region=water
O 8.9223159165 10.0510503418 8.4979612222 region=water
H 8.6876586212 9.8573326301 9.4281030569 region=water
H 8.0782938153 10.0737765524 8.0520178887 region=water
O 2.2086866602 0.4575366793 1.8603980911 region=water
H 2.7074405015 0.9170915286 2.5643863319 region=water
H 1.9449019090 10.6146598169 2.1989064344 region=water
O 3.7942526458 4.4013683386 7.6926555971 region=water
H 2.8019556823 4.4516703106 8.0538647583 region=water
H 4.2797472942 3.9292516279 8.4037455356 region=water
O 10.5839763961 9.6600871218 2.1047732424 region=water
H 0.1890294672 8.8503393773 2.1726331448 region=water
H 10.3896992409 10.0542858735 2.9942194997 region=water
O 4.2719055494 1.6354042019 3.2554358570 region=water
H 4.4992624119 1.6612851638 4.2258813340 region=water
H 5.0449911400 2.0950006142 2.8397138563 region=water
O 7.4600438154 10.0110540827 6.0828914016 region=water
H 7.9357661541 10.8809938929 6.1586539038 region=water
H 6.8944955680 10.0916816812 5.2309765492 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0 0 0 1
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0 1 0 0
35 36 1.0
35 37 1.0
38 39 1.0
38 40 1.0 -1 0 0
41 42 1.0
41 43 1.0
44 45 1.0
44 46 1.0
47 48 1.0 0 1 0
47 49 1.0 0 0 1
50 51 1.0
50 52 1.0
53 54 1.0
53 55 1.0
56 57 1.0
56 58 1.0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0 0 1 0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0
83 85 1.0
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0 1 0 0
95 97 1.0
98 99 1.0
98 100 1.0 0 0 -1
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0
116 118 1.0 0 -1 0
119 120 1.0
119 121 1.0
122 123 1.0 1 0 0
122 124 1.0
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Production, cumulative 300 ps
Provenance: `/home/ubuntu/work/03-production_workdir/prod_0300ps`
```ams
LoadSystem
File /home/ubuntu/work/03-production_workdir/prod_0250ps/ams.rkf
Section Molecule
End
MolecularDynamics
BinLog
DipoleMoment False
PressureTensor False
Time False
End
CalcPressure True
Checkpoint
Frequency 1000
End
CopyRestartTrajectory yes
NSteps 600000
Restart /home/ubuntu/work/03-production_workdir/prod_0250ps/ams.rkf
Thermostat
Tau 100.0
Temperature 380.0
Type NHC
End
TimeStep 0.5
Trajectory
SamplingFreq 200
WriteBonds True
WriteCharges True
WriteEngineGradients False
WriteMolecules True
WriteVelocities True
End
End
Task MolecularDynamics
System
Atoms
N 7.8476114248 3.2440313037 7.2146945844 region=glycine
C 8.5184080911 2.3879859765 8.2427186872 region=glycine
C 10.0080210162 2.0845541718 7.8849513465 region=glycine
O 10.5440643611 1.1817620180 8.4481533910 region=glycine
O 10.6670321163 2.8608571071 6.9533301758 region=glycine
H 7.5093715702 2.8421891859 6.3131255204 region=glycine
H 8.0988939179 4.1621019964 7.1786556754 region=glycine
H 7.9668183454 1.4571952417 8.2929554315 region=glycine
H 8.4091746536 2.8550661357 9.2392957844 region=glycine
H 9.9222915781 3.4814207610 6.7075470909 region=glycine
O 9.3362117422 7.5221735152 4.6315425795 region=water
H 9.7262660621 8.0817370974 5.2686058278 region=water
H 9.4453339328 7.9750854449 3.7981662326 region=water
O 4.2806646132 7.5190077509 9.4447405967 region=water
H 3.9140664756 6.7594793559 10.0357324061 region=water
H 3.5279078525 8.2049887725 9.3491546836 region=water
O 6.9024650935 5.2359878287 4.1223086332 region=water
H 7.7584588171 5.0760341303 3.8064612408 region=water
H 6.4149354945 4.5117607505 3.7343634149 region=water
O 8.9502910498 3.5232338449 10.7856977118 region=water
H 8.6835205864 4.4506595120 10.9377044041 region=water
H 9.9617169894 3.6322733929 10.7240191364 region=water
O 9.3491567208 5.4653035269 6.6960456725 region=water
H 9.5004368159 6.0054581260 5.9081088931 region=water
H 8.8032357018 5.9656343717 7.2762930177 region=water
O 7.7397169240 5.9819991470 0.6155817308 region=water
H 8.5707154068 6.4819921036 0.5928476008 region=water
H 7.3752933263 6.2102480873 10.6483638673 region=water
O 4.1822910982 9.5373399962 2.6617967704 region=water
H 4.5856364098 10.0535776025 1.8686934143 region=water
H 3.7550987575 8.7672344867 2.1849365318 region=water
O 6.4098014124 9.6216429835 4.4374921376 region=water
H 6.3679434503 8.8284798168 5.0861031219 region=water
H 6.0477337301 9.3501728470 3.5802531073 region=water
O 1.7456931982 9.9857312823 0.0214005511 region=water
H 2.4971595301 10.6651526360 0.1510087436 region=water
H 1.7930118835 9.7974084980 10.0893901572 region=water
O 1.6735847718 4.6163586138 8.9313715323 region=water
H 1.7089889058 3.6593187388 8.8207265456 region=water
H 2.3940307239 4.8629276989 9.5162992792 region=water
O 4.6828040152 0.3347401056 0.3325352165 region=water
H 4.7678101743 1.1181212461 0.9479629767 region=water
H 5.3428705372 0.6343612703 10.6666285861 region=water
O 0.1469046427 8.7528453414 6.5089086640 region=water
H 0.7875968102 9.1486109325 5.8806306815 region=water
H 0.5815869747 8.2204394644 7.1395508029 region=water
O 5.4020728600 2.5786639596 9.9341179326 region=water
H 4.4275415854 2.6562583726 10.1084407730 region=water
H 5.6662368730 3.3998781441 9.4054284962 region=water
O 3.9288791295 2.8885881334 5.4807833599 region=water
H 4.3383886297 2.0565038428 5.6676801746 region=water
H 4.6348312751 3.3169180749 4.8896741342 region=water
O 2.4696676456 10.3377318077 8.1714495584 region=water
H 2.9992648038 0.1036161538 8.4817148352 region=water
H 1.5531831937 10.6609992863 8.2314744665 region=water
O 9.0183002453 10.3547735353 10.3009790248 region=water
H 8.6176836578 9.8117731122 9.6004994378 region=water
H 9.4439727330 0.1197264994 9.7813190655 region=water
O 1.0064920988 1.3262024734 4.5787331894 region=water
H 1.1410785103 2.0732105413 3.9467569583 region=water
H 0.6644313856 1.7193931781 5.3823860989 region=water
O 5.5719346730 0.0815080445 8.4582000390 region=water
H 5.1208493412 0.1865007877 7.6146927008 region=water
H 5.3526050015 0.7556892193 9.0443462824 region=water
O 4.8931503898 3.9328953112 2.8142435746 region=water
H 4.6192632984 2.9826135529 2.6571147840 region=water
H 4.0116519869 4.3106941129 3.0792833932 region=water
O 1.8344175949 7.9153024954 2.0384724052 region=water
H 2.0276120496 8.4705107496 2.7916474028 region=water
H 1.6731276331 8.6468075616 1.3143034957 region=water
O 1.2658877493 7.4810276386 8.5783242421 region=water
H 1.5611057223 6.6688400008 8.2175496614 region=water
H 0.6698900296 7.3146325829 9.2790836204 region=water
O 0.9473786358 1.9848170021 0.9425378461 region=water
H 0.5067131076 2.8226377643 0.8502131586 region=water
H 1.7405476708 2.1238214521 1.4919843672 region=water
O 9.1993861662 3.7777100574 3.0332484539 region=water
H 9.1987024735 2.8410887167 3.3419727270 region=water
H 8.9982406268 3.8422334082 2.0546343574 region=water
O 9.3452661509 0.9986305417 3.7538974569 region=water
H 9.0483915983 0.2466074162 3.3250659542 region=water
H 10.2848535212 0.9522068035 3.6621557432 region=water
O 0.1980050140 4.6198124224 0.3136051326 region=water
H 10.7507894643 5.4615040625 0.5489358305 region=water
H 0.8138051533 4.7865195322 10.5694638879 region=water
O 6.9026538560 6.9463491236 9.2470577727 region=water
H 6.5932094267 6.2281528159 8.6604668301 region=water
H 5.9699975608 7.2703479105 9.4605146194 region=water
O 5.7629745590 4.5574756540 8.1613002192 region=water
H 4.8687607039 4.8676080269 7.6661810167 region=water
H 6.2059297448 3.8720345248 7.6611020035 region=water
O 7.1868863929 1.7905708584 1.0661608716 region=water
H 8.0677954423 2.1168660073 0.9787165950 region=water
H 6.7278659168 1.9932129152 0.2520568094 region=water
O 8.7995936192 9.2056909444 2.4303294753 region=water
H 7.9288033152 8.9382506268 2.5975289690 region=water
H 8.6360557471 9.7940583671 1.7555018042 region=water
O 5.5508296781 7.3197547068 5.7273867728 region=water
H 4.8829998665 6.9185643898 6.3052398928 region=water
H 6.0472293189 6.5108641440 5.3767088257 region=water
O 6.6546154937 1.6791851536 5.0412701724 region=water
H 5.9669115789 0.9973846269 5.3249740390 region=water
H 7.4375590679 1.2072395704 4.6980950889 region=water
O 3.3681434528 1.4167749523 2.8506571966 region=water
H 2.6283466109 1.0051643057 3.3165380618 region=water
H 4.0554357327 0.7306334684 3.1407842427 region=water
O 2.9766092267 1.7441668329 9.9156670649 region=water
H 3.2176056865 1.1690707589 10.7049004013 region=water
H 2.2110887309 2.2012847947 10.2293772842 region=water
O 3.4676232511 5.4088110260 6.7573824782 region=water
H 3.3709427999 4.5630194905 6.2609721025 region=water
H 2.7049479602 5.4446306021 7.3501063193 region=water
O 1.8878833881 9.8680863394 4.4983684270 region=water
H 1.8964216331 10.8188157527 4.6969502462 region=water
H 2.7762651904 9.7085710177 3.9645680744 region=water
O 4.2017141971 0.1002110267 5.9509568556 region=water
H 3.4645196217 10.5898786303 6.3591149113 region=water
H 4.7359569552 10.3097304303 5.7089181907 region=water
O 10.2012586102 7.3841199130 0.7166147136 region=water
H 9.5570312984 7.9561965879 1.0951402333 region=water
H 0.0782528964 7.7178849319 1.0503187973 region=water
O 3.9552958978 5.1748646937 0.0361931584 region=water
H 3.8024220352 4.9621288684 0.9658842701 region=water
H 4.3656814459 4.4012600720 10.6822694081 region=water
O 6.5513371423 7.3478765613 2.5643859420 region=water
H 6.9881005153 6.8515999915 1.8283537075 region=water
H 6.5246279360 6.5981590733 3.2599735333 region=water
O 2.6150296506 5.5319560812 2.7634730943 region=water
H 2.6062230590 6.2440247894 2.2050507943 region=water
H 1.6046140173 5.3916484312 2.9936969646 region=water
End
BondOrders
1 2 1.0
1 6 1.0
1 7 1.0
2 3 1.0
2 8 1.0
2 9 1.0
3 4 2.0
3 5 1.0
5 10 1.0
11 12 1.0
11 13 1.0
14 15 1.0
14 16 1.0
17 18 1.0
17 19 1.0
20 21 1.0
20 22 1.0
23 24 1.0
23 25 1.0
26 27 1.0
26 28 1.0 0 0 -1
29 30 1.0
29 31 1.0
32 33 1.0
32 34 1.0
35 36 1.0
35 37 1.0 0 0 -1
38 39 1.0
38 40 1.0
41 42 1.0
41 43 1.0 0 0 -1
44 45 1.0
44 46 1.0
47 48 1.0
47 49 1.0
50 51 1.0
50 52 1.0
53 54 1.0 0 1 0
53 55 1.0
56 57 1.0
56 58 1.0 0 1 0
59 60 1.0
59 61 1.0
62 63 1.0
62 64 1.0
65 66 1.0
65 67 1.0
68 69 1.0
68 70 1.0
71 72 1.0
71 73 1.0
74 75 1.0
74 76 1.0
77 78 1.0
77 79 1.0
80 81 1.0
80 82 1.0
83 84 1.0 -1 0 0
83 85 1.0 0 0 -1
86 87 1.0
86 88 1.0
89 90 1.0
89 91 1.0
92 93 1.0
92 94 1.0
95 96 1.0
95 97 1.0
98 99 1.0
98 100 1.0
101 102 1.0
101 103 1.0
104 105 1.0
104 106 1.0
107 108 1.0
107 109 1.0
110 111 1.0
110 112 1.0
113 114 1.0
113 115 1.0
116 117 1.0 0 -1 0
116 118 1.0 0 -1 0
119 120 1.0
119 121 1.0 1 0 0
122 123 1.0
122 124 1.0 0 0 -1
125 126 1.0
125 127 1.0
128 129 1.0
128 130 1.0
End
Lattice
10.9731013135 0.0000000000 0.0000000000
0.0000000000 10.9731013135 0.0000000000
0.0000000000 0.0000000000 10.9731013135
End
End
Engine ReaxFF
ForceField Glycine.ff
EndEngine
```
### Final MSD analysis
Provenance: `/home/ubuntu/work/03-production_workdir/msd_0300ps`
```ams
MeanSquareDisplacement
Atoms
Region glycine
end
ComputeStandardDeviation Yes
MaxFrame 200
Property DiffusionCoefficient
StartTimeSlope 5000.0
UseMolecularCentersOfMass
CheckForBondChanges Yes
Enabled Yes
end
end
Task MeanSquareDisplacement
TrajectoryInfo
Trajectory
KFFilename /home/ubuntu/work/03-production_workdir/prod_0300ps/ams.rkf
end
end
```
## Conclusion
The final glycine center-of-mass diffusion coefficient is **1.511364e-09 m^2/s** with a fitted MSD R^2 of 0.997441. The last three cumulative estimates are each within 15% of their mean, so the production estimate is converged by the specified test.
Note on AI-generated content¶
This page was generated by a Python script. That Python script was AI-generated.
All numbers, figures, and tables are extracted or postprocessed from actual AMS calculations, and can be transparently regenerated from the provided Python scripts.
Any scientific reasoning or citations was written by AI. This page is the actual one-shot output from using the ams2026 skill with an AI coding agent.