RISM-MOL-3D



= **RISM-MOL-3D** =

* Fast 3DRISM calculations * Solvation Free Energy and Partial Molar Volume calculations
 * Documentation**: [[file:doc.pdf]]

The Program is **Open Source** Please, read the license file:

Download the program & source code:


 * HOW TO CALCULATE Solvation Free Energy **

0) download

1) unpack         tar -xzf rism-mol-tools_2012_10_25.tar.gz

2) go to the folder         cd rism-mol-tools_2012_10_25

3) setup paths         export PATH=$PATH:$(pwd)             echo 'export PATH=$PATH:'$(pwd) >> .bashrc

4) create solvent files

assignSolventFF water.composition > water.rism createSlv water.composition water.rism > water.slv createOmega water.composition > waterOmega.txt

5) create solute input

Simplest example: echo 0 0 0 3.5 0.15 0 >file.rism

(first 3 columns - coordinates (Angstr), 4th - sigma (Angstr), 5th -epsilon (kcal/mol), 6th - charge (e))

More complicated: if you have pdb or xyz file (for example file.pdb), type coors2pat file.pdb > file.pat assignAtomTypes file.pat oplsaa.ff > file.at          createRismInput  file.pdb file.at oplsaa.ff > file.rism

6) run 3DRISM     multiGridMain parameters_fast.txt 'SoluteStructureFile="file.rism";'

7) calculate solvation free energy

calculateFreeEnergySimple file_in_water_

NOTE: if you want to run 3DRISM form other folder, you will need: 1) to copy water.slv to that folder     2) to copy parameters_fast.txt to that folder 3) to modify parameters_fast.txt to put full paths to the files at lines:              SolventOmegaFile="(full path to your RISM-MOL-Tools instalation)/waterOmega.txt";               SolventRDFsFile="(full path to your RISM-MOL-Tools instalation)/waterRDFs.txt";