modified on 19 October 2015 at 14:39 ••• 5,249 views

Release66:1D-RISM

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1D-RISM module in NWChem provide description of solvated systems following one-dimensional reference interaction site of model of Chandler and Anderson. Similar to ab-initio density-functional theory,  1D-RISM can be thought of as an approach where discrete particle representation of solvent degrees of freedom is replaced by average density field. Unlike traditional continuum solvation model, this density based representation is inherently inhomogenous and incorporates specific molecular features of the solvent.
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1D-RISM module in NWChem provides description of solvated systems following one-dimensional reference interaction site of model of Chandler and Anderson. Similar to ab-initio density-functional theory,  1D-RISM can be thought of as an approach where discrete particle representation of solvent degrees of freedom is replaced by average density field. Unlike traditional continuum solvation model, this density based representation is inherently inhomogenous and incorporates specific molecular features of the solvent. In the current implementation, 1D-RISM is not directly coupled to QM calculations but presumed to be used as a post processing step after QM calculations which provide ESP point charges for a given solute geometry.
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Then parameters for 1D-RISM calculations are defined in the rism input block
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rism
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  solute configuration <filename>
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  vdw [rule <arithmetic|geometric> ] parameters <filename>
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  [temp <float default 298.15>]
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  [closure <hnc|kh>]
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end
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 +
At this point energy task is supported, which is invoked using standard directive
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task rism energy
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* '''solute configuration'''  - points to the file that contains information about the solute geometry. charges, and atom type mapping. The format is similar to xyz style with additional fields that specify charge and atom type. The atom type maps back to the vdw parameter file (see below). The example file is shown below
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7
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O1        -1.092111    0.733461    1.237573  -1.104415 O
 +
O2          0.758765  -0.201687    0.473908  -1.043019 O
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C1        -0.212954    1.568653  -0.833617  -0.474263 C1
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C2        -0.174205    0.630432    0.357135  1.276672 C2
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H1          0.360636    1.160405  -1.668859  0.102898 H
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H2          0.242419    2.521128  -0.531952  0.118979 H
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H3        -1.243967    1.772778  -1.139547  0.123148 H
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* '''vdw''' - defines van der waals parameters
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** '''rule''' - optional setting that specifies combination rule, defaults to "arithmetic"
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** '''parameters''' - points to the file that contains vdw parameters for the system. Example file is shown below (note comments in the file)
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#Van der Waals parameters file for RISM
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# type  sigma(Angstrom) epsilon (kj/mol)
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C        0.3400E+01  0.3601E+00
 +
H        0.2600E+01  0.0628E-00
 +
 
 +
* '''temp'''  - defines temperature of the system with default value of 298.15
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* '''closure''' - specifies choice of closure
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 +
Upon completion of the run, the resulting  radial distribution functions are saved into rdf_out.data file.
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 +
The computed chemical potentials in both HNC and gaussian approximations are written in the output file.
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Here is the complete example input file for solvated calculation of acetic acid.
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echo
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start rism
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memory global 40 mb stack 23 mb heap 5 mb
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rism
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  closure kh
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  temp 298
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  vdw rule arithmetic parameters vdw.par
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  solute configuration solute2.data
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end
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task energy rism
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solute2.data file
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  8
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  O1        0.15566663    -0.86069508    1.9256322  -0.7323104568123959 O1
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  O2        2.31302544    -0.61550520    1.32869265  -0.7721248369124809 O2
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  C1        0.69252260    -1.26942616    -0.34814880  -0.4444201659837397 C1
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  C2        1.15967680    -0.88531805    1.02642840  1.004561861052242  C2
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  H1        0.22862001    -2.26160688    -0.31011132  0.1303963270585546 H
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  H2        -0.08170478    -0.56654621    -0.67834692  0.1513209389506027 H
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  H3        1.53138139    -1.28351200    -1.04644134  0.1454517042730594 H
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  H4        0.48680931    -0.66362820    2.83551288  0.5171246283741536 H4
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vdw.par file
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O1  3.0660  0.8809
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O2  2.9600  0.8792
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C1  3.4000  0.4580
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C2  3.4000  0.3601
 +
H  2.1150  0.0657
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H4  0.8000  0.1926

Latest revision as of 14:39, 19 October 2015


1D-RISM module in NWChem provides description of solvated systems following one-dimensional reference interaction site of model of Chandler and Anderson. Similar to ab-initio density-functional theory, 1D-RISM can be thought of as an approach where discrete particle representation of solvent degrees of freedom is replaced by average density field. Unlike traditional continuum solvation model, this density based representation is inherently inhomogenous and incorporates specific molecular features of the solvent. In the current implementation, 1D-RISM is not directly coupled to QM calculations but presumed to be used as a post processing step after QM calculations which provide ESP point charges for a given solute geometry.

Then parameters for 1D-RISM calculations are defined in the rism input block

rism
  solute configuration <filename>
  vdw [rule <arithmetic|geometric> ] parameters <filename> 
  [temp <float default 298.15>]
  [closure <hnc|kh>]
end

At this point energy task is supported, which is invoked using standard directive

task rism energy
  • solute configuration - points to the file that contains information about the solute geometry. charges, and atom type mapping. The format is similar to xyz style with additional fields that specify charge and atom type. The atom type maps back to the vdw parameter file (see below). The example file is shown below
7

O1         -1.092111    0.733461    1.237573  -1.104415 O
O2          0.758765   -0.201687    0.473908  -1.043019 O
C1         -0.212954    1.568653   -0.833617  -0.474263 C1
C2         -0.174205    0.630432    0.357135   1.276672 C2
H1          0.360636    1.160405   -1.668859   0.102898 H
H2          0.242419    2.521128   -0.531952   0.118979 H
H3         -1.243967    1.772778   -1.139547   0.123148 H
  • vdw - defines van der waals parameters
    • rule - optional setting that specifies combination rule, defaults to "arithmetic"
    • parameters - points to the file that contains vdw parameters for the system. Example file is shown below (note comments in the file)
#Van der Waals parameters file for RISM 
# type   sigma(Angstrom) epsilon (kj/mol)
C        0.3400E+01  0.3601E+00
H        0.2600E+01  0.0628E-00
  • temp - defines temperature of the system with default value of 298.15
  • closure - specifies choice of closure

Upon completion of the run, the resulting radial distribution functions are saved into rdf_out.data file.

The computed chemical potentials in both HNC and gaussian approximations are written in the output file.

Here is the complete example input file for solvated calculation of acetic acid.

echo
start rism

memory global 40 mb stack 23 mb heap 5 mb

rism
  closure kh
  temp 298
  vdw rule arithmetic parameters vdw.par
  solute configuration solute2.data
end

task energy rism

solute2.data file

 8
 
 O1         0.15566663    -0.86069508     1.9256322   -0.7323104568123959 O1
 O2         2.31302544    -0.61550520     1.32869265  -0.7721248369124809 O2
 C1         0.69252260    -1.26942616    -0.34814880  -0.4444201659837397 C1
 C2         1.15967680    -0.88531805     1.02642840   1.004561861052242  C2
 H1         0.22862001    -2.26160688    -0.31011132   0.1303963270585546 H
 H2        -0.08170478    -0.56654621    -0.67834692   0.1513209389506027 H
 H3         1.53138139    -1.28351200    -1.04644134   0.1454517042730594 H
 H4         0.48680931    -0.66362820     2.83551288   0.5171246283741536 H4

vdw.par file

O1  3.0660  0.8809
O2  2.9600  0.8792
C1  3.4000  0.4580
C2  3.4000  0.3601
H   2.1150  0.0657
H4  0.8000  0.1926