# Example: 3D-RISM: Glycine¶

Download 3DRISM-Glycine.run

#! /bin/sh

# == 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.

# == Remarks for different solvent than water ==

# The default values for the RISM1D subblock key are only applicable if the
# solvent is water. You must change the FLUIDPARAM subkey of the subblock key
# RISM1D when modeling a different solvent, at least the dielectric constant and
# the density. In that case you may also have to change other subkeys of the
# subblock key RISM1D. For a different solvent than water, of course, you also
# have to change the description of the subblock SOLVENT. You may have to change
# the boxsize.

$ADFBIN/adf << eor Title 3D-RISM test SYMMETRY C(s) NOBECKEGRID ATOMS internal C 0 0 0 0.0 0.0 0.0 SigU=3.50 EpsU=0.066 O 1 0 0 1.208031 0.0 0.0 SigU=2.96 EpsU=0.200 O 1 2 0 1.341959 123.553475 0.0 SigU=2.96 EpsU=0.200 C 1 2 3 1.495685 124.769221 180.0 SigU=3.50 EpsU=0.066 N 4 1 2 1.427005 115.495309 0.0 SigU=3.25 EpsU=0.170 H 3 1 2 0.992780 105.645766 0.0 SigU=1.00 EpsU=0.046 H 4 1 2 1.107716 107.591718 123.973836 SigU=1.00 EpsU=0.046 H 4 1 2 1.107716 107.591718 -123.973836 SigU=1.00 EpsU=0.046 H 5 4 1 1.028574 109.800726 57.697485 SigU=1.00 EpsU=0.046 H 5 4 1 1.028574 109.800726 -57.697485 SigU=1.00 EpsU=0.046 End Basis Type DZP Core small End XC LDA End RISM glycine 1N RISM1D subend SOLVENT1 water UNITS uWeight=g/mol ULJsize=A ULJenergy=kcal/mol Ucoord=A Udens=1/A3 Parameters Weight=18.015 nAtoms=2 1 -0.8476 3.166 0.1554 0.000000 0.00000 0.000000 2 0.4238 1.000 0.0460 -0.816490 0.00000 0.577359 0.816490 0.00000 0.577359 DenSpe=0.03333 SUBEND SOLUTE CO BOXSIZE 32.0 32.0 32.0 BOXGRID 64 64 64 SUBEND END Gradient eor # The densf utility can be used to convert the 3D-RISM grid data stored in the TAPE21 file to # the TAPE41 format suitable for visualization by ADFview. The following fields are created # for each solvent site: Huv (solvent total correlation function), Uuv (solvent potential in RT), # Guv (solvent pair distribution function), Cuv (solvent direct correlation), # and PMF (potentials of mean force in kcal/mol)$ADFBIN/densf << eor
RISM
eor

mv TAPE41 glycine.t41
mv TAPE21 glycine.t21
rm -f RISMDATA