MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, powerful atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out. The basic example demonstrates some of these features.

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MDAnalysis can be easily installed with its dependencies using the pip or conda package managers; MDAnalysis is also available in some recent Linux distributions.

All source code is available under the GNU General Public License, version 2 (or any later version at your choice) from and the Python Package index


Ask questions on the GitHub Discussions forum and be part of the conversation. You can also join the MDAnalysis Discord Server to talk with other users and developers. (In order to join our Discord server, use the invitation link

Please report bugs or enhancement requests through the Issue Tracker.

MDAnalysis is open source and welcomes your contributions. Fork the repository on GitHub and submit a pull request. Participate on the GitHub Discussions (Development) forum.

MDAnalysis regularly takes part in various mentoring and outreach programs, such as Google Summer of Code, Google Season of Docs, Outreachy, the Station1 Frontiers Fellowship, and the CompChemURG mentorship schemes. Many of the current core developers joined the project through these mentoring schemes. The project also frequently offers teaching workshops, both online and in-person; recordings are often made available on the MDAnalysis YouTube channel. Follow our blog, LinkedIn, Twitter, and Bluesky pages for updates on how to participate.

To connect with other MDAnalysis users, present your work using MDAnalysis, and meet the developer team, join us August 21-23, 2024 for our User Group Meeting in London, United Kingdom.


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