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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

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.


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

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

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


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.

.. Links

.. _`10.1002/jcc.21787`:
.. _GNU Public Licence, version 2:
.. _Issue Tracker:
.. _`mdnalysis-discussion mailing list`:
.. _`online documentation`:
.. _`Table of Supported Coordinate Formats`:
.. _`atom selection commands`:
.. _`Selection exporters`:
.. _NumPy:
.. _Amber:
.. _NAMD:
.. _Gromacs:
.. _VMD:
.. _PyMOL:
.. _PDB:
.. _XYZ format:

.. _Unit Tests:
.. _MDAnalysisTests:

.. _`easy_install`:
.. _`pip`:

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