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 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
