================================ MDAnalysis Repository README

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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 topology formats. MDAnalysis also includes widely used analysis algorithms in the MDAnalysis.analysis module.

.. _numfocus-fiscal-sponsor-attribution:

The MDAnalysis project uses an open governance model_ and is fiscally sponsored by NumFOCUS. Consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

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This project is bound by a Code of Conduct_.

Example analysis script

.. 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.center_of_mass())

Documentation

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 User Guide_.

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.

Installation and availability

The latest release can be installed via pip or conda as 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_).

Contributing

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 developer guide.

Citation

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:10.25080/Majora-629e541a-00e_

• 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_

For citations of included algorithms and sub-modules please see the references_.

.. Footnotes

.. [*] 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 .. _LICENSE: https://github.com/MDAnalysis/mdanalysis/blob/master/LICENSE .. _Installation Quick Start: https://www.mdanalysis.org/pages/installation_quick_start/ .. _MDAnalysis.analysis: https://docs.mdanalysis.org/documentation_pages/analysis_modules.html .. _tutorials: https://userguide.mdanalysis.org/examples/README.html .. _videos: https://www.mdanalysis.org/pages/learning_MDAnalysis/#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/documentation_pages/references.html

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