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A python wrapper around the Gromacs tools.

Project description

Build Status Code Coverage Documentation Latest release on zenodo (with DOI) PRs Welcome!

A primitive wrapper around the Gromacs tools until we have proper python bindings. It also provides a small library (cook book) of often-used recipes and helper functions to set up MD simulations.

Documentation is mostly provided through the python doc strings and available at https://gromacswrapper.readthedocs.org for recent releases.

The source code is available in the GromacsWrapper git repository.

Please be aware that this is alpha software that most definitely contains bugs. It is your responsibility to ensure that you are running simulations with sensible parameters.

Licence

The GromacsWrapper package is made available under the terms of the GNU Public License v3 (or any higher version at your choice) except as noted below. See the file COPYING for the licensing terms for all modules.

The distribution contains third party software that is copyrighted by the authors but distributed under licences compatible with this package license. Where permitted and necessary, software/files were modified to integrate with GromacsWrapper.

Installation

Releases

The latest version of GromacsWrapper from PyPi and can be installed with

pip install GromacsWrapper

Development version

The master branch in the GitHub source repository generally contains useful code but nevertheless, things can break in weird and wonderful ways. Please report issues through the Issue Tracker and mention that you used the develop branch.

To use the development code base: checkout the master branch:

git clone https://github.com/Becksteinlab/GromacsWrapper.git
cd GromacsWrapper

and install

python setup.py install

Download and Availability

The GromacsWrapper home page is http://github.com/Becksteinlab/GromacsWrapper. The latest release of the package is being made available from https://github.com/Becksteinlab/GromacsWrapper/releases

You can also clone the GromacsWrapper git repository or fork for your own development:

git clone git://github.com/Becksteinlab/GromacsWrapper.git

Questions

Please ask questions in the Issue Tracker (instead of private email).

Reporting Bugs and Contributing to GromacsWrapper

Please use the Issue Tracker to report bugs, installation problems, and feature requests.

Pull requests for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a general introduction on how make a pull request and contribute to open source projects.

Building Documentation

Install Sphinx:

pip install sphinx

and compile:

cd package/doc/sphinx
make html

Python 3

Python 3 support is currently in alpha state; in principle it is fully supported but if you find bugs please report them through the Issue Tracker.

Citing

Latest release on zenodo (with DOI)

GromacsWrapper was written by Oliver Beckstein with contributions from many other people. Please see the file AUTHORS for all the names.

If you find this package useful and use it in published work I’d be grateful if it was acknowledged in text as

“… used GromacsWrapper (Oliver Beckstein et al, https://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)”

or in the Acknowledgements section.

Thank you.

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
GromacsWrapper-0.7.0-py2.py3-none-any.whl (631.4 kB) Copy SHA256 hash SHA256 Wheel py2.py3 Aug 9, 2018
GromacsWrapper-0.7.0.tar.gz (625.7 kB) Copy SHA256 hash SHA256 Source None Aug 9, 2018

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