A Python package for setup and analysis of parallel tempering and replica exchange molecular dynamics

This is a package with many tools, functions, and some classes for analyzing and running molecular dynamics trajectories. It is specifically designed for working with Replica Exchange Molecular Dynamics (Parallel Tempering, when the replicas are at different temperatures). It is, in-part, specialized for analyzing trajectories of TADDOL-catalyzed reactions, though most components are general.

Installing

To install, run:

git clone https://github.com/theavey/ParaTemp.git
cd ParaTemp
pip install -e .

or this should work using conda (based on this gist):

git clone https://github.com/theavey/ParaTemp.git
cd ParaTemp
conda install --yes --file requirements.txt
python setup.py install

Notes

All simulations have so far been from GROMACS, but with the powerful generality of MDAnalysis, that should not be a particular constraint for using many of the analysis components of this package.

This package depends on MDAnalysis, NumPy, pandas, panedr, and gromacswrapper. The dependencies are listed in requirements.txt. They all should be installable with conda or pip.

With recent updates to MDAnalysis, this should now be compatible with Python 2.7 and Python 3.4+. This is currently tested on Python 2.7 and 3.6.