mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

MDAnalysis

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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.

… 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_.

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If you use MDAnalysis_ in your project consider letting your users and the world know about it by displaying the MDAnalysis_ badge! Embedding code_ is available for different markups.

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 packaged under the
GNU General Public License, version 3 or any later version. Invidiual
source code components are provided under a mixture of GPLv3+ compatible
licenses, including LGPLv2.1+ and GPLv2+. Please see the file LICENSE_
for more information.

Contributing

Please report bugs or enhancement requests through the Issue Tracker. Questions can also be asked on GitHub Discussions.

If you are a new developer who would like to start contributing to
MDAnalysis get in touch on GitHub Discussions. 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_