Example: load atom types from a previous runΒΆ

You can load the atom types from another force field calculation.

Observe that this is done with the LoadForceFieldAtomTypes inside the System block, see the System definition section of the AMS manual.

Download LoadTypes.run

#!/bin/sh

# In this example we use the amber forcefield that cannot guess atom types

# First we "calculate" the types

# We do this by specifying them as atom attributes (ForceField.Type)

export AMS_JOBNAME=CalculateTypes

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams << eor
Task GeometryOptimization

Properties Charges=yes

System
   Atoms
     C       1.94807   3.58290  -0.58162       ForceField.Charge=0.0       ForceField.Type=CT
     H       1.69949   4.49893  -1.05273       ForceField.Charge=0.0       ForceField.Type=HC
     H       2.99455   3.17964  -0.86304       ForceField.Charge=0.0       ForceField.Type=HC
     C       0.94659   2.40054  -0.92364       ForceField.Charge=0.0       ForceField.Type=CT
     C       1.94191   3.61595   1.09448       ForceField.Charge=0.0       ForceField.Type=CT
     N      -1.74397  -3.46417   0.31178       ForceField.Charge=-0.9530   ForceField.Type=N2
     C      -1.00720  -2.20758   0.33536       ForceField.Charge=0.8185    ForceField.Type=CA
     C      -1.66928  -1.00652   0.31001       ForceField.Charge=-0.5215   ForceField.Type=CM
     C      -0.92847   0.25653   0.34895       ForceField.Charge=0.0053    ForceField.Type=CM
     N       0.43971   0.26735   0.38232       ForceField.Charge=-0.0484   ForceField.Type=N*
     N       0.36409  -2.20477   0.28992       ForceField.Charge=-0.7584   ForceField.Type=NC
     C       1.09714  -0.95413   0.22469       ForceField.Charge=0.7538    ForceField.Type=C
     H      -2.89781  -3.50815   0.31746       ForceField.Charge=0.4234    ForceField.Type=H
     H      -1.21484  -4.49217   0.31721       ForceField.Charge=0.4234    ForceField.Type=H
     H      -2.80940  -0.93497   0.30550       ForceField.Charge=0.1928    ForceField.Type=HA
     H      -1.55324   1.21497   0.33885       ForceField.Charge=0.1958    ForceField.Type=H4
     C       1.23309   1.44017   0.30994       ForceField.Charge=0.0066    ForceField.Type=CT
     O       2.58277  -1.01636   0.23914       ForceField.Charge=-0.6252   ForceField.Type=O
     H       2.37276   1.25557   0.29984       ForceField.Charge=0.2902    ForceField.Type=H2
     O       1.02358   2.43085   1.50880       ForceField.Charge=-0.2033   ForceField.Type=OS
     H       1.17136   1.95097  -1.87367       ForceField.Charge=0.0       ForceField.Type=HC
     H      -0.10600   2.77333  -0.80348       ForceField.Charge=0.0       ForceField.Type=HC
     H       1.62170   4.54039   1.51392       ForceField.Charge=0.0       ForceField.Type=H1
     H       2.99608   3.28749   1.41345       ForceField.Charge=0.0       ForceField.Type=H1
   End
End

Engine ForceField
   Type Amber95
EndEngine

eor


# Now we load the types from the previous result

# The result should be identical to the first calculation

export AMS_JOBNAME=LoadTypes

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams << eor
Task GeometryOptimization

System
   Atoms
     C       1.94807   3.58290  -0.58162
     H       1.69949   4.49893  -1.05273
     H       2.99455   3.17964  -0.86304
     C       0.94659   2.40054  -0.92364
     C       1.94191   3.61595   1.09448
     N      -1.74397  -3.46417   0.31178
     C      -1.00720  -2.20758   0.33536
     C      -1.66928  -1.00652   0.31001
     C      -0.92847   0.25653   0.34895
     N       0.43971   0.26735   0.38232
     N       0.36409  -2.20477   0.28992
     C       1.09714  -0.95413   0.22469
     H      -2.89781  -3.50815   0.31746
     H      -1.21484  -4.49217   0.31721
     H      -2.80940  -0.93497   0.30550
     H      -1.55324   1.21497   0.33885
     C       1.23309   1.44017   0.30994
     O       2.58277  -1.01636   0.23914
     H       2.37276   1.25557   0.29984
     O       1.02358   2.43085   1.50880
     H       1.17136   1.95097  -1.87367
     H      -0.10600   2.77333  -0.80348
     H       1.62170   4.54039   1.51392
     H       2.99608   3.28749   1.41345
   End
   LoadForceFieldCharges    file=CalculateTypes.results
   LoadForceFieldAtomTypes  file=CalculateTypes.results
End

Engine ForceField
   Type Amber95
   Verbosity Verbose

EndEngine

eor