=====================
  MDAnalysis README
=====================

MDAnalysis_ is a Python toolkit to analyze molecular dynamics
trajectories generated by CHARMM, Amber, NAMD, LAMMPS, or Gromacs.

.. _MDAnalysis: https://www.mdanalysis.org

It allows one to read molecular dynamics trajectories and access the
atomic coordinates through numpy arrays. This provides a flexible and
relatively fast framework for complex analysis tasks. In addition,
CHARMM-style atom selection commands are implemented. Trajectories can
also be manipulated (for instance, fit to a reference structure) and
written out.

Code is hosted at https://github.com/MDAnalysis/mdanalysis

The Online Documentation is available at https://docs.mdanalysis.org

For installation instruction please have a look at INSTALL and the
instructions online at https://github.com/MDAnalysis/mdanalysis/wiki/Install



License
=======

This software is copyright 
(c) 2005 Naveen Michaud-Agrawal
(c) 2006 Naveen Michaud-Agrawal and Elizabeth J. Denning
(c) 2007-2009 Naveen Michaud-Agrawal, Elizabeth J. Denning, and Oliver Beckstein
(c) 2010-2016 The MDAnalysis Development Team and all contributors
              listed in the file AUTHORS
unless stated otherwise in the source files.

MDAnalysis is released under the GPL software license, version 2, with
the following exceptions (see AUTHORS and LICENSE for details):

- The DCD reading/writing code is licensed under the UIUC Open Source
  License.

- The Gromacs xdrlib code for accessing Gromacs trajectories is used
  under a "BSD-2-clause" licence.

- The transformations module was written by Christoph Gohlke and is
  used under a "BSD-3-clause" licence.

- The pyqcprot code was written by Joshua Adelman and licensed under a
  "BSD-3-clause" licence.

All licenses, including disclaimer, are available in the 'LICENSE'
file.

Citation
=========

When using MDAnalysis in published work, please cite the following
two papers:

    R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,
    M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,
    S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:
    A Python package for the rapid analysis of molecular
    dynamics simulations. In S. Benthall and S. Rostrup,
    editors, Proceedings of the 15th Python in Science
    Conference, pages 102-109, Austin, TX, 2016. SciPy.

    N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and
    O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular
    Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327.
    doi: 10.1002/jcc.21787

    https://www.mdanalysis.org

Included algorithms
-------------------

A number of algorithms are included in MDAnalysis and
MDAnalysis.analysis that have been published separately. Please cite
the appropriate paper as listed at
https://docs.mdanalysis.org/documentation_pages/references.html#citations-for-included-algorithms-and-modules



Contact 
=======

Please report bugs and feature requests through the Issue Tracker at

     https://github.com/MDAnalysis/mdanalysis/issues

Help is also available through the mailing list

     http://groups.google.com/group/mdnalysis-discussion

