pygromacs

Some simple tools designed to generate input files for the molecular dynamics package Gromacs.

Planned features

• Read .mdp configuration files and quickly generate many new ones with specified options changed.
• Also .top topology files!
• Convolute sets of generated topologies and configuration files to prepare runs for a large parameter space.

Development status

Just about nothing is finished.

• MDP file tools
  • File class
  • Generation tools
• Topology file tools
  • File class
  • Generation tools
• Tools for cross producing run input files far from done

Installation

Currently only Python 3.4 is supported, while a workaround for redirect_stdout is implemented. Also, there's currently nothing to install. In theory:

python setup.py install

Documentation

Documentation is available at Read the Docs: http://pygromacs.readthedocs.org/

To install the local theme, see: https://github.com/snide/sphinx_rtd_theme

[] (https://coveralls.io/r/pjohansson/pygromacs?branch=working)

Links

http://www.gromacs.org/