modified on 19 October 2015 at 13:39 ••• 5,514 views

Release66:1D-RISM

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Line 4: Line 4:
  rism
  rism
 +
  solute configuration <filename>
 +
  vdw [rule <arithmetic|geometric> ] parameters <filename>
   [temp <float default 298.15>]
   [temp <float default 298.15>]
-
   [closure <hnc|kh>
+
   [closure <hnc|kh>]
-
  [vdw [rule <arithmetic|geometric> ] parameters <filename> ]
+
  end
  end
-
* '''temp'''  - defines temperature of the system with default value of 298.15
+
* '''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
-
* '''closure''' - specifies choice of closure
+
 
 +
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
* '''vdw''' - defines van der waals parameters
** '''rule''' - optional setting that specifies combination rule, defaults to "arithmetic"
** '''rule''' - optional setting that specifies combination rule, defaults to "arithmetic"
Line 16: Line 27:
  #Van der Waals parameters file for RISM  
  #Van der Waals parameters file for RISM  
-
  # name   sigma(Angstrom) epsilon (kj/mol)
+
  # type   sigma(Angstrom) epsilon (kj/mol)
  C        0.3400E+01  0.3601E+00
  C        0.3400E+01  0.3601E+00
  H        0.2600E+01  0.0628E-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

Revision as of 15:45, 29 September 2015


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. In the current implementation, 1D-RISM is not directly coupled to QM calculations but presumed to be use as a post processing step after QM calculations which provide ESP point charges for a given solute geometry

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