/SolvationToolkit

In-house tools for setting up arbitrary (currently non-water) solute-solvent mixtures for simulation in GROMACS

Primary LanguagePythonGNU Lesser General Public License v2.1LGPL-2.1

##Build Status

Build Status

SolvationToolkit

Tools for setting up arbitrary (currently non-water) solute-solvent mixtures for simulation in GROMACS or AMBER formats.

At this point what's here consists primarily of solvationtoolkit.solvated_mixtures which sets up a class structure to use openmoltools (and related utilities) to automatically set up simulations of mixtures of solvents/solutes, and scripts/start.py which gives an example driver script using this to set up simulations of several mixtures. Automated testing is also implemented.

Prerequisites

  • Auto-installable:
    • openmoltools v0.6.5 or later
    • mdtraj (via omnia channel on conda)
    • OpenEye tools
    • packmol (via omnia channel on conda)
    • ParmEd

Issues

  • See issue tracker

Disclaimers

  • This code is currently in approximately beta release status. Use at your own risk. We will almost certainly be making changes to the API in the near future.