# Example: 3D-RISM: Glycine¶

Download 3DRISM-Glycine.run

Expert option

Computing solvent effects with the 3D-RISM model is illustrated on the glycine example.

All subkeys in the RISM block are discussed in the User’s Guide. The things to pay attention to here are SigU and EpsU parameters for each atom in the ATOMS block, the solvent parameters in the SOLVENT sub-block and the FFT box parameters in the SOLUTE sub-block. Both SigU and EpsU values as well as the solvent parameters may be obtained from force field parameter lists. Parameters for some common solvents are available in the ADF User’s Guide.

One should take into account the following when choosing FFT box parameters in the SOLUTE block:

• the box should be at least twice as large as your model in each dimension,
• the number of grid points in each dimension must be a power of 2, and
• accuracy of the results and the memory usage depend on the number of grid-points

Note: the 3D-RISM part in ADF has not been parallelized, thus calculating on more than 1 processor will not reduce the elapsed time. In this example only the gradients are calculated, no geometry optimization is performed.

\$ADFBIN/adf -n1 << eor
Title 3D-RISM test

SYMMETRY C(s)

NOBECKEGRID

Define
rco=1.208031
rcoh=1.341959
rcc=1.495685
rcn=1.427005
roh=0.992780
rch1=1.107716
rnh1=1.028574
aoco=123.553475
acco=124.769221
ancc=115.495309
ahoc=105.645766
ach1=107.591718
ah1=109.800726
dch1=123.973836
dh1=57.697485
dc=180.
dn=0.0
doh=0.0
End

ATOMS  internal
C   0  0  0   0.00  0.00     0.00     SigU=3.50    EpsU=0.066
O   1  0  0   rco   0.00     0.00     SigU=2.96    EpsU=0.200
O   1  2  0   rcoh  aoco     0.00     SigU=2.96    EpsU=0.200
C   1  2  3   rcc   acco     dc       SigU=3.50    EpsU=0.066
N   4  1  2   rcn   ancc     dn       SigU=3.25    EpsU=0.170
H   3  1  2   roh   ahoc     doh      SigU=1.00    EpsU=0.046
H   4  1  2   rch1  ach1     dch1     SigU=1.00    EpsU=0.046
H   4  1  2   rch1  ach1    -dch1     SigU=1.00    EpsU=0.046
H   5  4  1   rnh1  ah1      dh1      SigU=1.00    EpsU=0.046
H   5  4  1   rnh1  ah1     -dh1      SigU=1.00    EpsU=0.046
End

Basis
Type DZP
Core small
End

XC
LDA
End
RISM glycine 1N
RISM1D
subend

SOLVENT water
UNITS      uWeight=g/mol  ULJsize=A  ULJenergy=kcal/mol Ucoord=A Udens=1/A3
Parameters Weight=18.015   nAtoms=2
1    -0.8476   3.166    0.1554       0.000000  0.00000  0.000000
2     0.4238   1.000    0.0460      -0.816490  0.00000  0.577359
0.816490  0.00000  0.577359
DenSpe=0.03333
SUBEND

SOLUTE  CO
BOXSIZE 32.0 32.0 32.0
BOXGRID   64   64   64
SUBEND
END