A python wrapper around the gromacs tools.
Project description
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 an optional analysis module with plugins for more complicated analysis tasks.
Documentation is mostly provided through the python doc strings and available at http://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 vmd module is made available under the LGPL v3 (see COPYING and COPYING.LESSER). numkit is provided under the “Modified BSD Licence” (as it contains some code from scipy).
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 develop 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 develop branch:
git clone https://github.com/Becksteinlab/GromacsWrapper.git cd GromacsWrapper git checkout -b develop origin/develop
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
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.
Building Documentation
Install Sphinx:
apt-get install python-sphinx
and compile:
cd package/doc/sphinx make html
Citing
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, http://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)”
or in the Acknowledgements section.
Thank you.
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