README
1=====================
2 MDAnalysis README
3=====================
4
5MDAnalysis_ is a Python toolkit to analyze molecular dynamics
6trajectories generated by CHARMM, Amber, NAMD, LAMMPS, or Gromacs.
7
8.. _MDAnalysis: https://www.mdanalysis.org
9
10It allows one to read molecular dynamics trajectories and access the
11atomic coordinates through numpy arrays. This provides a flexible and
12relatively fast framework for complex analysis tasks. In addition,
13CHARMM-style atom selection commands are implemented. Trajectories can
14also be manipulated (for instance, fit to a reference structure) and
15written out.
16
17Code is hosted at https://github.com/MDAnalysis/mdanalysis
18
19The Online Documentation is available at https://docs.mdanalysis.org
20
21For installation instruction please have a look at INSTALL and the
22instructions online at http://wiki.mdanalysis.org/INSTALL
23
24
25
26License
27=======
28
29This software is copyright
30(c) 2005 Naveen Michaud-Agrawal
31(c) 2006 Naveen Michaud-Agrawal and Elizabeth J. Denning
32(c) 2007-2009 Naveen Michaud-Agrawal, Elizabeth J. Denning, and Oliver Beckstein
33(c) 2010-2016 The MDAnalysis Development Team and all contributors
34 listed in the file AUTHORS
35unless stated otherwise in the source files.
36
37MDAnalysis is released under the GPL software license, version 2, with
38the following exceptions (see AUTHORS and LICENSE for details):
39
40- The DCD reading/writing code is licensed under the UIUC Open Source
41 License.
42
43- The Gromacs xdrlib code for accessing Gromacs trajectories is used
44 under a "BSD-2-clause" licence.
45
46- The transformations module was written by Christoph Gohlke and is
47 used under a "BSD-3-clause" licence.
48
49- The pyqcprot code was written by Joshua Adelman and licensed under a
50 "BSD-3-clause" licence.
51
52All licenses, including disclaimer, are available in the 'LICENSE'
53file.
54
55Citation
56=========
57
58When using MDAnalysis in published work, please cite the following
59two papers:
60
61 R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy,
62 M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski,
63 S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis:
64 A Python package for the rapid analysis of molecular
65 dynamics simulations. In S. Benthall and S. Rostrup,
66 editors, Proceedings of the 15th Python in Science
67 Conference, pages 102-109, Austin, TX, 2016. SciPy.
68
69 N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and
70 O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular
71 Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327.
72 doi: 10.1002/jcc.21787
73
74 https://www.mdanalysis.org
75
76Included algorithms
77-------------------
78
79A number of algorithms are included in MDAnalysis and
80MDAnalysis.analysis that have been published separately. Please cite
81the appropriate paper as listed at
82https://docs.mdanalysis.org/documentation_pages/references.html#citations-for-included-algorithms-and-modules
83
84
85
86Contact
87=======
88
89Please report bugs and feature requests through the Issue Tracker at
90
91 https://github.com/MDAnalysis/mdanalysis/issues
92
93Help is also available through the mailing list
94
95 http://groups.google.com/group/mdnalysis-discussion
96
97