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.

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

SYMMETRY C(s)

NOBECKEGRID

Geometry
  Branch Old
End

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

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.