Example: 3D-RISM: Glycine¶
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 Gradient End input eor rm TAPE21 logfile
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.