Example: 3D-RISM: Glycine¶
#! /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 adf.SigU and EpsUadf. 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 adf.SigU and EpsUadf. 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
# 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.
$AMSBIN/ams <<eor
System
atoms
C 0.0 0.0 0.0 adf.SigU=3.50 adf.EpsU=0.066
O 1.208031058311462 0.0 0.0 adf.SigU=2.96 adf.EpsU=0.200
O -0.741720974445343 1.118348836898804 0.0 adf.SigU=2.96 adf.EpsU=0.200
C -0.8529478907585144 -1.228639006614685 0.0 adf.SigU=3.50 adf.EpsU=0.066
N -0.1451586186885834 -2.467742681503296 0.0 adf.SigU=3.25 adf.EpsU=0.170
H -0.09300804138183594 1.869869947433472 0.0 adf.SigU=1.00 adf.EpsU=0.046
H -1.528575420379639 -1.167157530784607 0.8756611347198486 adf.SigU=1.00 adf.EpsU=0.046
H -1.528575420379639 -1.167157530784607 -0.8756611347198486 adf.SigU=1.00 adf.EpsU=0.046
H 0.4767249822616577 -2.513782262802124 0.8179888725280762 adf.SigU=1.00 adf.EpsU=0.046
H 0.4767249822616577 -2.513782262802124 -0.8179888725280762 adf.SigU=1.00 adf.EpsU=0.046
end
end
Task SinglePoint
Properties
Gradients Yes
End
Engine ADF
title 3D-RISM test
basis
core small
type DZP
end
nobeckegrid
Relativity Level=None
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
symmetry C(s)
xc
lda
end
EndEngine
eor
# The densf utility can be used to convert the 3D-RISM grid data stored in the adf.rkf file to
# the TAPE41 format suitable for visualization by AMSview. 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)
$AMSBIN/densf << eor
adffile ams.results/adf.rkf
RISM
eor