[gmx-developers] Calculating Solvent-Solvent and Solute-Solvent Interaction Energies

Jackson ChiefElk jchiefel at ucsc.edu
Wed Nov 19 02:50:11 CET 2014

Hello.  I have developed 2 programs, for use in my own research, and I am
making them available for everybody.  These programs have been used to
calculate solvent-solvent, and solute-solvent interaction energies inside
of confined environments, from Gromacs MD simulations.

The source code I've made available on GitHub, the links are below. I've
used the programs to calculate water-water, and water-ligand interaction
energies inside of cyclodextrin, and a pore in the beta-adrenergic
receptor.  To use this program, Gromacs has to be installed. These programs
were written for users with installs less than 5.0, but I am making changes
in the source to do the calculations for users that have versions >= 5.0.
Tested compilation with with gcc and clang. Shell scripts in each Git, are
program specific, so make sure (.xtc) and (.tpr) from simulation is in the
same directory as the compiled C program and shell scripts. Also require a
distance file(.txt), calculated using g_dist. I will make an instructional
guide soon, when I get a website up.  Email me if you are interested in
using this in your research, website will not be up for 2 weeks.

SOLUTE-Solvent Program

Solvent-Solvent Program

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