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