Skip to content
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
129 changes: 52 additions & 77 deletions index.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,93 +7,68 @@ title: MDAnalysis
<img src="{{ site.baseurl }}/public/mdanalysis-logo_square.png"
style="float: right" alt="MDAnalysis" width="30%"/>

**MDAnalysis** is an object-oriented Python library to analyze
trajectories from molecular dynamics (MD) simulations in [many popular
formats]({{site.pypi.docs}}/documentation_pages/coordinates/init.html#id1). It
can write most of these formats, too, together with [atom
selections]({{site.pypi.docs}}/documentation_pages/selections_modules.html#selection-exporters)
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](https://numpy.org/) arrays. This provides a flexible and
relatively fast framework for complex analysis tasks. In addition,
powerful atom
[selection commands]({{site.pypi.docs}}/documentation_pages/selections.html)
are implemented. Trajectories can also be manipulated (for instance,
fit to a reference structure) and written out. The
[basic example]({{ site.baseurl }}/pages/basic_example) demonstrates some
of these features.

Read more:

* [installation quick start]({{ site.baseurl }}/pages/installation_quick_start)
* [learning MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis)

Also, check out the [blog]({{ site.baseurl }}/blog) or subscribe to our
[news feed]({{ site.baseurl }}/{{site.feed.path}}) to follow development
updates and events.

## Availability ##

MDAnalysis can be [**easily
installed**]({{site.baseurl}}/pages/installation_quick_start/) 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](https://www.gnu.org/licenses/gpl-2.0.html)
(or any later version at your choice) from
[github.com/MDAnalysis/mdanalysis](https://github.com/MDAnalysis/mdanalysis)
and the Python Package index
[pypi.org/project/MDAnalysis](https://pypi.org/project/MDAnalysis).

## Participating ##

Ask **questions** on the [{{ site.mailinglists.discussion.name }}
forum]({{ site.mailinglists.discussion.url }}) and **be part of the
conversation**. You can also join the [{{ site.discord.name }}
Discord Server]({{ site.discord.url }}) to talk with other users and
developers. (In order to join our Discord server, use the invitation link
[{{ site.discord.invite }}]({{ site.discord.invite }}).)

Please report **bugs** or **enhancement requests** through the [Issue
Tracker]({{ site.github.issues }}).

MDAnalysis is **open source** and welcomes *your* contributions. [Fork
the repository on
GitHub](https://github.com/MDAnalysis/mdanalysis#fork-destination-box)
and submit a pull request. Participate on the [{{
site.mailinglists.developer.name }}
forum]({{ site.mailinglists.developer.url }}).

MDAnalysis regularly takes part in various **mentoring and outreach programs**, such as [Google Summer of Code](https://summerofcode.withgoogle.com/), [Google Season of Docs](https://developers.google.com/season-of-docs), [Outreachy](https://www.outreachy.org/), the [Station1 Frontiers Fellowship](https://www.station1.org/sff), and the [CompChemURG](https://www.bindingsites.co.uk/home) mentorship schemes. Many of the [current core developers](/about/#mdanalysis-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](https://www.youtube.com/@mdanalysis3040). Follow our [blog]({{ site.baseurl }}/blog), [LinkedIn](https://www.linkedin.com/company/mdanalysis/), [Twitter](https://twitter.com/mdanalysis), and [Bluesky](https://bsky.app/profile/mdanalysis.bsky.social) pages for updates on how to participate.


## Supporting ##

If you like MDAnalysis and want to support our mission, please
consider making a donation to support our efforts.
The **MDAnalysis Project** develops open-source tools for the analysis of molecular simulation data, providing researchers with efficient and accessible solutions for studying molecular structures and dynamics.

{{ site.numfocus.donate_button }}
MDAnalysis is a fiscally sponsored project of [NumFOCUS][], a nonprofit that promotes open practices in research, data, and scientific computing.

At the core of the project is *MDAnalysis*, **an open-source Python library** for analyzing molecular dynamics (MD) trajectories across [multiple formats]({{ site.docs.userguide.url }}/formats/index.html#formats). *MDAnalysis* enables seamless reading and writing of simulation data, allowing users to efficiently analyze molecular structures and dynamics, including particle-based trajectories and individual coordinate frames (e.g., biomolecules in the [PDB format][]).

With *MDAnalysis*, you can access atomic coordinates as [NumPy][] arrays, providing a flexible and efficient framework for complex analysis tasks. The library includes powerful [atom selection commands]({{ site.docs.userguide.url }}/selections.html) for extracting subsets of structures and supports trajectory transformations (e.g., fitting to a reference structure).

Learn more about our **mission, development, team, and governance** on the [About MDAnalysis]({{ site.baseurl }}/about/) page.

## Get Started

If you're new to *MDAnalysis*, explore the following resources to install the `MDAnalysis` package, access tutorials, and dive into the documentation:

- [Getting Started]({{ site.baseurl }}/pages/getting_started/)
- [Learning MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis)
- [Documentation]({{ site.baseurl }}/pages/documentation)

## Community

MDAnalysis is driven by an active **community of users and contributors**. Stay updated and get involved through the following pages:

<!-- TODO: Add link [Get Involved]({{ site.baseurl }}/pages/about/#get-involved)
-->
- [Community]({{ site.baseurl }}/pages/community/) &mdash; Get involved, ask questions, and collaborate.
- [Blog]({{ site.baseurl }}/blog) &mdash; Stay updated with development news and community highlights.
- [Events]({{ site.baseurl }}/pages/events/) &mdash; Join workshops, conferences, and mentoring programs.

## Contributing

Want to contribute to MDAnalysis? Here’s how:

(Donations are made through [our fiscal sponsor][], [NumFOCUS][], which is
a 501(c)(3) non-profit charity in the United States; as such,
donations to NumFOCUS are tax-deductible as allowed by law. As with
any donation, you should consult with your personal tax adviser or the
IRS about your particular tax situation.)
- [Contribute]({{ site.baseurl }}/pages/contribute/) &mdash; Learn how to help improve MDAnalysis through coding, documentation, or discussions.
- [MDAKits and MDA-based tools]({{ site.baseurl }}/pages/mdakits/) &mdash; Build and extend MDAnalysis with MDAKits.
- [Support MDAnalysis financially](#funding--support) &mdash; Donate via NumFOCUS to sustain the project.


## Citing MDAnalysis

If you use MDAnalysis in your research, please cite it appropriately and consider displaying our MDAnalysis badge in your projects. All citation formats and badge instructions are available in our [Citation guidelines]({{ site.baseurl }}/pages/citations/).

Additionally, consider displaying our badge in your projects that use MDAnalysis. We provide several [embedding markup examples]({{ site.baseurl }}/pages/citations/#powered-by-mdanalysis).

[![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)
Additionally, consider displaying our badge in your projects that use
MDAnalysis. We provide several [embedding markup examples]({{ site.baseurl }}/pages/citations/#powered-by-mdanalysis).

## Funding & Support

If you find MDAnalysis useful and would like to support its continued development, please consider making a donation. You can learn more about out Sponsors in our [Funding]({{ site.baseurl }}/pages/funding/) page.

{{ site.numfocus.donate_button }}

<small>
Donations are made through [our fiscal sponsor][], [NumFOCUS][], which is a 501(c)(3) non-profit charity in the United States; as such, donations to NumFOCUS are tax-deductible as allowed by law. As with any donation, you should consult with your personal tax adviser or the IRS about your particular tax situation.
</small>

<a href="https://github.com/MDAnalysis/mdanalysis"><img style="position: absolute; top:
0; right: 0; border: 0;"
src="https://camo.githubusercontent.com/a6677b08c955af8400f44c6298f40e7d19cc5b2d/68747470733a2f2f73332e616d617a6f6e6177732e636f6d2f6769746875622f726962626f6e732f666f726b6d655f72696768745f677261795f3664366436642e706e67"
alt="Fork me on GitHub"
data-canonical-src="https://s3.amazonaws.com/github/ribbons/forkme_right_gray_6d6d6d.png"></a>


[NumFOCUS]: https://www.numfocus.org
[our fiscal sponsor]: {{site.baseurl}}/about#partners
[NumPy]: https://numpy.org/
[PDB format]: https://www.wwpdb.org/documentation/file-format
Loading