KIT-MBS/pyrexMD

Workflow-orientated python package for Replica Exchange Molecular Dynamics

About pyrexMD

pyrexMD is a Python package that is mainly designed for research projects which

• use (contact-guided) Replica Exchange Molecular Dynamics or (contact-guided) Molecular Dynamics
• or focus on structure analyses and comparison.

It has three main goals:

1. Interactive 'all-purpose' environment. By including various modified GROMACS and MDAnalysis Python bindings, this package provides a comprehensive Jupyter notebooks based environment to design, run, and analyze MD simulation projects from beginning to end.
2. Data visualization is important. In pyrexMD, most analysis functions for calculating useful quantities, such as root-mean-square deviation (RMSD), Q values, contact distances, etc., can generate specialized figures in the same step by passing the keyword argument plot=True.
3. User-friendly and simple application. Where possible, the provided functions combine individual steps into comprehensive workflows with additional automation features. It is possible to rapidly create whole setup or structure-analysis workflows within a few commands, thereby significantly enhancing productivity and reducing the time spent on various stages of the project.

pyrexMD makes it straightforward to create, share, and reproduce research results or transfer the work to other biomolecular structures of interest. Furthermore, it lowers the technical barrier for non-specialists who want to use Replica Exchange for enhanced sampling.

pyrexMD should be used with Jupyter notebooks and requires GROMACS to run MD simulations.

Documentation

You can access the documentation via https://kit-mbs.github.io/pyrexMD/
and the quick guide via https://kit-mbs.github.io/pyrexMD/quick_guide.html.

Installation Instructions

(1) Install MPI:

On ubuntu:

sudo apt-get install openmpi-bin libopenmpi-dev

On macOS:

brew install mpich

(2) Download and install an MPI-enabled version of GROMACS following the instructions given below:

https://manual.gromacs.org/documentation/current/index.html

(3) Download and install the pyrexMD package:

git clone https://github.com/KIT-MBS/pyrexMD.git
cd pyrexMD
python -m pip install .

(4) Enable the trajectory viewer for Jupyter:

jupyter nbextension enable --py widgetsnbextension
jupyter nbextension enable --py nglview

Tests

To run the Python tests with code coverage, go into the pyrexMD folder and run:

coverage run -m pytest
coverage report html

Open htmlcov with any browser to see the code coverage, e.g.:

firefox htmlcov/index.html

Examples

To run one of the short examples, go into the pyrexMD/examples folder and run:

jupyter notebook

Participating

pyrexMD is free and open source. It is published under the MIT license. We welcome your contribution so feel free to ask questions, report bugs, fork, etc.

Citation

Voronin et al., (2021). pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics. Journal of Open Source Software, 6(68), 3325, https://doi.org/10.21105/joss.03325

bibtex entry:

@article{Voronin2021,
doi = {10.21105/joss.03325},
url = {https://doi.org/10.21105/joss.03325},
year = {2021},
publisher = {The Open Journal},
volume = {6},
number = {68},
pages = {3325},
author = {Arthur Voronin and Alexander Schug},
title = {{pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics}},
journal = {Journal of Open Source Software}
}

License

MIT License

Copyright (c) 2021 KIT-MBS

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.