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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, DL_Poly, HooMD, LAMMPS and many others — see the lists of supported
trajectory formats_ and
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
tax-deductible donation to 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_.
If you use MDAnalysis_ in your project consider lettting your users and the world know about it by displaying the MDAnalysis_ badge!
Embedding code_ is available for different markups.
.. code:: python
import MDAnalysis as mda
u = mda.Universe('topol.tpr','traj.trr')
ag = u.select_atoms('name OH')
ag.positions ag.velocities ag.forces
for ts in u.trajectory: print(ag.center_of_mass())
New users should read the
Quickstart Guide_ and might want to
look at our videos_, in which core developers explain various aspects
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
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.
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.
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/documentation_pages/coordinates/init.html#id1
.. _topology formats: https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats
.. _MDAnalysis: https://www.mdanalysis.org
Installation Quick Start:
User Guide: https://userguide.mdanalysis.org
MDAnalysis API docs:
Issue Tracker: https://github.com/mdanalysis/mdanalysis/issues
user mailing list:
developer mailing list:
.. _references: https://docs.mdanalysis.org/documentation_pages/references.html
.. _Embedding code: https://www.mdanalysis.org/pages/citations/#powered-by-mdanalysis
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