MDAnalysis

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In-person participants at the MDAnalysis 2025 User Group Meeting (online participants not shown).

The 2025 MDAnalysis User Group Meeting wrapped up. If you want to see what great talks and workshops we had, have a look at the UGM2025 repo github.com/MDAnalysis/U... . It was fantastic to have so many of you in Arizona and joining online! See you all again soon.

Lillian Chong in front of her opening slide.

Today's fantastic keynote "From Protein Structure to Function: Weighted Ensmebles Beyon Machine Learning" by Lillian Chong.

Matthias Heyden of Arizona State University presenting in front of a screen with multiple protein structures where dynamics are indicated by arrows.

Yesterday's keynote speaker Matthias Heyden on "Sub-Picosecond Timescale Information in Microsecond Simulations".

Our MDAnalysis User Group Meeting 2025 is in full swing in sunny Arizona ! www.mdanalysis.org/pages/ugm2025/

We’ve updated the MDAnalysis Code of Conduct (CoC) by adopting the @numfocus.bsky.social CoC to support a more impartial and transparent process.

Read more:
👉 www.mdanalysis.org/2025/11/07/N...

Thanks to our community for helping us keep things respectful, inclusive, and welcoming. 🧡

It's ligand-focussed day at the #CCPBioSim training week, and we've been using @openforcefield.org & @openmm.org to parameterise and run protein-ligand MD, and @mdanalysis.bsky.social & ProLIF for analysis! #compchem

We're happy to announce the new 2.10.0 release of the MDAnalysis library www.mdanalysis.org/2025/10/26/r...

It contains performance improvements, more parallel analysis tools, and the IMDv3 stream reader for directly processing running simulations.

Thanks to 25 contributors, 16 of which were new!

Dr. Matthias Heyden, Associate Professor, Arizona State University. Prof. Heyden's research group studies the dynamics and function of biomolecules with molecular simulations and Monte Carlo simulations. A special interest of his is anharmonic low-frequency vibrations, which are easily excitable by molecular collisions and can exhibit large deviations from harmonic approximations.

Matthias Heyden focuses on anharmonic low-frequency vibrations, which play a critical role in #molecular behavior but are often overlooked in harmonic models. His talk will show how sub-picosecond data can reveal key insights — and how data #streaming via #MDAnalysis makes it possible.

Dr. Lillian Chong, Professor, University of Pittsburgh. Prof. Chong's research focuses on developing and applying advanced simulation methods to investigate rare but biologically important events, with an emphasis on capturing rigorous kinetics. Her group leads the development of the open-source WESTPA software, which implements weighted ensemble path sampling strategies for efficient simulation of rare events. She also works on the development of implicitly polarized force fields and rational design of protein conformational switches.

@ltchong.bsky.social develops methods to simulate rare but important biological events — leading the team behind @westpasoftware.bsky.social, an #OSS for weighted ensemble (WE) path sampling. Her talk will explore how #WE methods and #ML can uncover hidden protein states and rare transitions.

🧵 In this thread, we introduce Lillian Chong (Univ. of Pittsburgh) and Matthias Heyden (ASU) as keynote speakers for the #mdaUGM2025! Register now to hear these talks on novel molecular simulation and analysis strategies.

📅 Nov 9–11
📍 Arizona State University
🔗 www.mdanalysis.org/2025/07/15/u...

MDAnalysis User Group Meeting (logo)

Come to the @mdanalysis.bsky.social User Group Meeting at Arizona State University in November. See www.mdanalysis.org/2025/07/15/u... for our keynote speakers and more updates.

Great opportunity for junior researchers to present their work and to network with the MDAnalysis community.

🗞️ Good news! Abstract and travel bursary applications for #mdaUGM2025 (Nov 9–11 @ ASU) are still being accepted — registration is now on a rolling basis.

Details and a link to the registration form are found on the #MDAnalysis blog: www.mdanalysis.org/2025/07/15/u...

#MolecularDynamics #OpenSource

🚨 Deadline coming up!
🎯 Don’t miss your chance to present at the #mdaUGM2025 — abstract + travel bursary applications due July 15!

Meet the community, share your work, learn from others, and get support to attend.

🔗 Info: www.mdanalysis.org/pages/ugm2025/

#MDAnalysis #OSS #MolecularDynamics #UGM

MDAnalysis UGM logo

#mdaUGM2025 is officially happening! Abstracts and travel bursary applications are being accepted from now until the July 15, 2025 deadline: www.mdanalysis.org/2025/04/13/u....

🗓️ November 9-11, 2025
📍Tempe, Arizona, USA (and online)

#open-source-software #molecular #simulations #streaming

WESTPA logo

Do you like coding in #Python? Have you been using #MonteCarlo methods or running #MD simulations?

Working with MDAnalysis and @westpasoftware.bsky.social on a GSoC 2025 project may be just for you! For details, read our blog post: www.mdanalysis.org/2025/02/28/g....

Pre-proposal deadline: Mar 21

Friendly reminder that this is the last week to submit your pre-proposals if you are interested in working with MDAnalysis in the GSoC 2025 program (⏱️ **Deadline: March 21st**). Read our GSoC blog post for full details: www.mdanalysis.org/2025/02/28/g....

MDAnalysis 2.9.0 (and its blog post) is out: www.mdanalysis.org/2025/03/11/r...!

Includes:
* Additional Gromacs/distopia/parallel analysis support
* New "water"/"precision" keywords

🙏 to the release's 10 contributors (3 new), and to @numfocus.bsky.social/@chanzuckerberg.bsky.social for support.

Google Summer of Code logo

MDAnalysis is participating in Google Summer of Code 2025! Do you like #coding to solve problems in #biophysics #chemistry or #materials?

Read our blog on how to apply: www.mdanalysis.org/2025/02/28/g.... Pre-proposals are due March 21st.

We value transparency; please communicate in public forums.

Making the image not transparent (sorry!) actually shows you the simple Python code that one uses to generate it: Make a MDAnalysis AtomGroup and call the visualize() method.

Visualization of part of a protein with MDAnalysis and Blender/MolecularNodes together with Python code to generate the image.

🎉 Small Development Grant by @numfocus.bsky.social for Advanced Molecular Visualizations with #MolecularNodes and @blender3d.bsky.social! @yuxuanzhuang.bsky.social and @bradyajohnston.bsky.social will build an API & integrate with @projectjupyter.bsky.social. See www.mdanalysis.org/2024/12/12/s...

We released MDAnalysis 2.8.0 🚀 See the blog post www.mdanalysis.org/2024/11/22/r... . Highlights: (1) all code under the GNU Lesser General Public License, (2) new Guesser API, (3) general parallelization for analysis tools, (3) DSSP analysis class, (4) more MDAKits.

Your opinion matters! 🌟 If you haven't already, please take a moment to share your thoughts about MDAnalysis communications and resources: www.mdanalysis.org/2024/07/31/s....

The survey deadline is August 31st.

Do you use or contribute to MDAnalysis? Have you attended MDAnalysis events? We invite all community members to participate in a survey before Aug 31 to help us foster an inclusive and supportive community and develop a communications strategy: www.mdanalysis.org/2024/07/31/s.... Thanks in advance!

⏰ It's almost that time for the #mdaUGM2024 registration deadline (July 14, midnight anywhere on Earth). Sign up now to secure your spot: www.mdanalysis.org/pages/ugm202...

We look forward to seeing you there!

MDAnalysis UGM 2024

🚨 There is only ~1 week left to register for the #mdaUGM2024 before the deadline, July 14th!

Register now to join us in London Aug 21-23 for exciting talks, interesting discussions and an interactive hackathon related to all things #MD and #OSS: mdanalysis.org/pages/ugm202...

group photo from the MDAnalysis/MolSSI Workshop at ASU, June 24-25, 2024

Greetings from the joint MDAnalysis / MolSSI hybrid workshop at ASU: from users to developers in the analysis of molecular simulations with software engineering best practices and MDAKits mdanalysis.org/2024/05/14/A... : ~45 in-person attendees+instructors and ~80 online.

📢 One of MDAnalysis's very own core developers, Richard Gowers, will be giving a CCPBioSim industry talk June 19th, from 14:00-15:30 BST. Read more and access the link to register in our latest blog post: www.mdanalysis.org/2024/05/30/c....

Google Summer of Code logo

Outreachy logo

MDAnalysis is thrilled to be working with 4 amazing new contributors through the @ggl.bsky.social Summer of Code and Outreachy programs. Meet them all and learn more about the projects they will be working on over the next few months in our new blog post: www.mdanalysis.org/2024/05/27/g...

📢📢 Registration for #mdaUGM2024 is now open! Join us in London from 21-23 Aug to talk about all things MDAnalysis. You also won't want to miss the talks from our keynote speakers, Drs. Antonia Mey and Francesca Stanzione.

Register now to secure your place:
www.mdanalysis.org/pages/ugm202...