MDAnalysis is a Python library to analyze molecular dynamics trajectories.
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MDAnalysis_ is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists.
It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DLPoly, HooMD, LAMMPS and many others — see the lists of supported
topology formats. MDAnalysis also includes widely used analysis algorithms in the
The MDAnalysis project uses an
open governance model_ and is fiscally sponsored by
NumFOCUS. Consider making a
tax-deductible donationto help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
.. image:: https://www.mdanalysis.org/public/images/numfocus-sponsored-small.png :alt: NumFOCUS (Fiscally Sponsored Project) :target: https://numfocus.org/project/mdanalysis :align: center
This project is bound by a
Code of Conduct_.
.. code:: python
import MDAnalysis as mda
# Load simulation results with a single line u = mda.Universe('topol.tpr','traj.trr')
# Select atoms ag = u.select_atoms('name OH')
# Atom data made available as Numpy arrays ag.positions ag.velocities ag.forces
# Iterate through trajectories for ts in u.trajectory: print(ag.centerofmass())
New users should read the
Quickstart Guide_ and might want to look at our videos_, in which core developers explain various aspects of MDAnalysis.
All users should read the
Developers may also want to refer to the
MDAnalysis API docs_.
A growing number of
tutorials_ are available that explain how to conduct RMSD calculations, structural alignment, distance and contact analysis, and many more.
The latest release can be installed via
condaas described in the
Installation Quick Start_.
Source code is hosted in a git repository at https://github.com/MDAnalysis/mdanalysis and is available under the GNU General Public License, version 2 (see the file LICENSE_).
Please report bugs or enhancement requests through the
Issue Tracker. Questions can also be asked on the
user mailing list.
If you are a new developer who would like to start contributing to MDAnalysis get in touch on the
developer mailing list. To set up a development environment and run the test suite read the
When using MDAnalysis in published work, please cite the following two papers:
R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. doi:
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:
For citations of included algorithms and sub-modules please see the references_.
..  *build: Unit testing is for the whole package; **coverage is shown for the core library modules and the analysis modules.
.. NumFOCUS: https://numfocus.org/ .. _open governance model: https://www.mdanalysis.org/about/#governance .. _tax-deductible donation: https://numfocus.org/donate-to-mdanalysis .. _
Code of Conduct: https://www.mdanalysis.org/pages/conduct/ .. _trajectory formats: https://docs.mdanalysis.org/documentationpages/coordinates/init.html#id1 .. topology formats: https://docs.mdanalysis.org/documentationpages/topology/init.html#supported-topology-formats .. MDAnalysis: https://www.mdanalysis.org .. _LICENSE: https://github.com/MDAnalysis/mdanalysis/blob/master/LICENSE .. _
Installation Quick Start: https://www.mdanalysis.org/pages/installationquickstart/ .. _
MDAnalysis.analysis: https://docs.mdanalysis.org/documentationpages/analysismodules.html .. _
tutorials: https://userguide.mdanalysis.org/examples/README.html .. _
videos: https://www.mdanalysis.org/pages/learningMDAnalysis/#videos ..
Quickstart Guide: https://userguide.mdanalysis.org/examples/quickstart.html .. _
User Guide: https://userguide.mdanalysis.org .. _
MDAnalysis API docs: https://docs.mdanalysis.org .. _
Issue Tracker: https://github.com/mdanalysis/mdanalysis/issues .. _
user mailing list: https://groups.google.com/group/mdnalysis-discussion .. _
developer guide: https://userguide.mdanalysis.org/contributing.html .. _
developer mailing list: https://groups.google.com/group/mdnalysis-devel .. _
10.1002/jcc.21787: https://dx.doi.org/10.1002/jcc.21787 .. _
10.25080/Majora-629e541a-00e: https://doi.org/10.25080/Majora-629e541a-00e .. _references: https://docs.mdanalysis.org/documentationpages/references.html
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