README: GromacsWrapper

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.

See INSTALL for installation instructions. Documentation is mostly provided through the python doc strings. See Download and Availability for download instructions if the instructions in INSTALL are not sufficient.

The source code is also 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).

Included Software

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.

In case of problems please direct error reports to Oliver Beckstein in the first instance as these bugs might not have been present in the original software or files.

Included third party content:

GridMat-MD

• Grid-based Membrane Analysis Tool for use with Molecular Dynamics [Allen2009]
• version: 1.0.2
• license: GPL 3.0
• W. J. Allen, J. A. Lemkul, and D. R. Bevan. (2009) “GridMAT-MD: A Grid-based Membrane Analysis Tool for Use With Molecular Dynamics.” J. Comput. Chem. 30 (12): 1952-1958.
• http://bevanlab.biochem.vt.edu/GridMAT-MD/

odict.py

• a simple implementation of an ordered dictionary as proposed in PEP 0372
• copyright: (c) 2008 by Armin Ronacher and PEP 273 authors.
• license: modified BSD license (compatible with GPL)
• http://dev.pocoo.org/hg/sandbox/raw-file/tip/odict.py

gromacs.fileformats.preprocess

• The preprocessor is based on pypreprocessor.py from pypreprocessor, release 0.4.0.
• copyright: (c) 2010 Evan Plaice
• license: MIT (compatible with GPL)
• http://code.google.com/p/pypreprocessor/

Citing

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, http://github.com/orbeckst/GromacsWrapper)”

or in the Acknowledgements section.

If you use the gridmatmd plugin also cite [Allen2009].

Thank you.

References

[Allen2009]

(1, 2) W. J. Allen, J. A. Lemkul, and D. R. Bevan. (2009) “GridMAT-MD: A Grid-based Membrane Analysis Tool for Use With Molecular Dynamics.” J. Comput. Chem. 30, 1952-1958.

Download and Availability

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

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

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

Contact

Please use the Issue Tracker to report bugs and feature requests; general feedback and inquiries can be sent to Oliver Beckstein by e-mail.