Release66:1D-RISM
From NWChem
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__NOTITLE__ | __NOTITLE__ | ||
- | 1D-RISM module in NWChem | + | 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 | Then parameters for 1D-RISM calculations are defined in the rism input block | ||
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* '''temp''' - defines temperature of the system with default value of 298.15 | * '''temp''' - defines temperature of the system with default value of 298.15 | ||
* '''closure''' - specifies choice of closure | * '''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 |
Latest revision as of 13:39, 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