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An object-oriented toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.

Project description

.. Summary for PyPI
.. http://pypi.python.org/pypi/MDAnalysis/

MDAnalysis_ is an object-oriented python toolkit to analyze molecular
dynamics trajectories generated by CHARMM_, Gromacs_, Amber_, NAMD_, or
LAMMPS_; it also reads other formats (e.g. PDB_ files and `XYZ format`_
trajectories; see the `Table of Supported Coordinate Formats`_ for details). It
can write most of these formats, too, together with atom selections for use in
Gromacs_, CHARMM_, VMD_ and PyMOL_ (see `Selection exporters`_).

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. Fairly complete
`atom selection commands`_ are implemented. Trajectories can
also be manipulated (for instance, fit to a reference structure) and
written out in a range of formats.

Availability
============

**Source code** is available from http://www.mdanalysis.org under the
`GNU Public Licence, version 2`_, together with the `online
documentation`_. **Packages** can be downloaded from

http://pypi.python.org/pypi/MDAnalysis/

or installed/upgraded via PyPI (using either `easy_install`_ or `pip`_)::

easy_install -U MDAnalysis
pip install --upgrade MDAnalysis

Please report **bugs** or **enhancement requests** through the `Issue
Tracker`_. Questions can also be asked on the `mdnalysis-discussion mailing
list`_.

In order to run the `Unit Tests`_ it is also necessary to install a
separate package MDAnalysisTests_ containing the test and test
data. As it contains about 18 MB of molecular dynamics trajectories
and simulation system structures it is not included with the library
itself.


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`_


.. Links

.. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787
.. _GNU Public Licence, version 2: http://www.gnu.org/licenses/old-licenses/gpl-2.0.html
.. _Issue Tracker: http://code.google.com/p/mdanalysis/issues/list
.. _`mdnalysis-discussion mailing list`:
http://groups.google.com/group/mdnalysis-discussion
.. _`online documentation`:
http://pythonhosted.org//MDAnalysis/
.. _`Table of Supported Coordinate Formats`:
http://pythonhosted.org//MDAnalysis/documentation_pages/coordinates/init.html#id1
.. _`atom selection commands`:
http://pythonhosted.org//MDAnalysis/documentation_pages/selections.html#selection-commands
.. _`Selection exporters`:
http://pythonhosted.org//MDAnalysis/documentation_pages/selections_modules.html#selection-exporters
.. _NumPy: http://numpy.scipy.org
.. _CHARMM: http://www.charmm.org/
.. _Amber: http://ambermd.org/
.. _LAMMPS: http://lammps.sandia.gov/
.. _NAMD: http://www.ks.uiuc.edu/Research/namd/
.. _Gromacs: http://www.gromacs.org/
.. _VMD: http://www.ks.uiuc.edu/Research/vmd/
.. _PyMOL: http://www.pymol.org/
.. _PDB: http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
.. _XYZ format: http://openbabel.org/wiki/XYZ_%28format%29

.. _Unit Tests: https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests
.. _MDAnalysisTests: https://github.com/MDAnalysis/mdanalysis/wiki/MDAnalysisTests

.. _`easy_install`: http://packages.python.org/distribute/easy_install.html
.. _`pip`: http://www.pip-installer.org/en/latest/index.html

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