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

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

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 and documentation are hosted at

    http://code.google.com/p/mdanalysis/

The Online Documentation is available at

    http://mdanalysis.googlecode.com/git/package/doc/html/index.html 

The html manual is also located in the docs/ directory of the source
distribution.

For installation instruction please have a look at INSTALL and the
instructions online at http://code.google.com/p/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) 2010-2012 Naveen Michaud-Agrawal, Elizabeth J. Denning, and Oliver Beckstein
              and persons 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 libxdr code for accessing Gromacs trajectories including our
  modifications is published under the Lesser GNU Public Licence
  (LGPL).

- The KDTree and neigbour-searching code is Thomas Hamelryck's code
  from the Biopython module (with minor modifications) and is used
  under the terms of the Biopython license.

- 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

    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

    http://mdanalysis.googlecode.com

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

If you use the RMSD alignment code that uses the QCProt module please also cite

    Douglas L. Theobald. Rapid calculation of RMSD using a
    quaternion-based characteristic polynomial. Acta Crystallographica
    A 61 (2005), 478--480.

    Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald. Fast
    determination of the optimal rotational matrix for macromolecular
    superpositions. J. Comput. Chem. 31 (2010), 1561--1563.

If you use the helix analysis algorithm HELANAL in MDAnalysis.analysis.helanal
please cite

    Bansal M, Kumar S, Velavan R. HELANAL - A program to characterise
    helix geometry in proteins. J. Biomol. Struct. Dyn. 17 (2000),
    811--819

If you use the GNM trajectory analysis code in MDAnalysis.analysis.gnm
please cite

    Benjamin A. Hall, Samantha L. Kaye, Andy Pang, Rafael Perera, and
    Philip C. Biggin. Characterization of Protein Conformational
    States by Normal-Mode Frequencies. JACS 129 (2007), 11394--11401.

Thanks! 



Contact 
=======

Please report bugs and feature requests through the Issue Tracker at

     http://code.google.com/p/mdanalysis/issues/

Help is also available through the mailing list

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

For anything that cannot be resolved through the Issue Tracker or the
mailing list please get in touch with one of the primary developers:

- Naveen Michaud-Agrawal <naveen.michaudagrawal@gmail.com>
- Elizabeth Denning <denniej0@gmail.com> 
- Oliver Beckstein <orbeckst@gmail.com>
