mdanalysis

by MDAnalysis

MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

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MDAnalysis Repository README

|numfocus| |build| |cov| [*]_

|docs| |devdocs| |usergroup| |developergroup| |anaconda| |mybinder|

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

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.

.. 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
_.

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.centerofmass())

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/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/installation
quickstart/ .. _
MDAnalysis.analysis
: https://docs.mdanalysis.org/documentation
pages/analysismodules.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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