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mdanalysis.bsky.social
MDAnalysis
@mdanalysis.bsky.social
390 followers 33 following 47 posts
Working with data in the molecular sciences. https://www.mdanalysis.org
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mdanalysis.bsky.social
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.
In-person participants at the MDAnalysis 2025 User Group Meeting (online participants not shown).
November 12, 2025 at 12:09 AM
mdanalysis.bsky.social
Today's fantastic keynote "From Protein Structure to Function: Weighted Ensmebles Beyon Machine Learning" by Lillian Chong.
Lillian Chong in front of her opening slide.
November 10, 2025 at 9:14 PM
mdanalysis.bsky.social
Yesterday's keynote speaker Matthias Heyden on "Sub-Picosecond Timescale Information in Microsecond Simulations".
Matthias Heyden of Arizona State University presenting in front of a screen with multiple protein structures where dynamics are indicated by arrows.
November 10, 2025 at 4:30 PM
mdanalysis.bsky.social
Our MDAnalysis User Group Meeting 2025 is in full swing in sunny Arizona ! www.mdanalysis.org/pages/ugm2025/
November 10, 2025 at 4:25 PM
mdanalysis.bsky.social
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. 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.
July 18, 2025 at 2:39 PM
mdanalysis.bsky.social
@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.
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.
July 18, 2025 at 2:34 PM
mdanalysis.bsky.social
#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
MDAnalysis UGM logo
May 20, 2025 at 6:24 PM
mdanalysis.bsky.social
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
WESTPA logo
March 19, 2025 at 8:51 AM
mdanalysis.bsky.social
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.
Google Summer of Code logo
March 3, 2025 at 8:17 AM
mdanalysis.bsky.social
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.
December 12, 2024 at 8:47 PM
mdanalysis.bsky.social
🎉 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...
Visualization of part of a protein with MDAnalysis and Blender/MolecularNodes together with Python code to generate the image.
December 12, 2024 at 8:42 PM
mdanalysis.bsky.social
🚨 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...
MDAnalysis UGM 2024
July 8, 2024 at 10:42 AM
mdanalysis.bsky.social
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.
group photo from the MDAnalysis/MolSSI Workshop at ASU, June 24-25, 2024
June 25, 2024 at 11:03 PM
mdanalysis.bsky.social
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...
Google Summer of Code logo Outreachy logo
May 29, 2024 at 2:16 PM
mdanalysis.bsky.social
Register for our joint MDAnalysis/MolSSI workshop at Arizona State University on June 24th-25th 2024. Attendance is free, travel bursaries are available, register for in-person or online attendance at www.mdanalysis.org/2024/05/14/A... Registration deadline is soon, May 27, 2024.
MDAnalysis Workshop June 24-25th 2024, Arizona State University. Stylized saguaro cactus with flowers shaped like the MDAnalysis logo.
May 14, 2024 at 9:18 PM
mdanalysis.bsky.social
Save the date: June 24th & 25th: Joint MDAnalysis/MolSSI workshop at Arizona State University. Details to follow.

www.mdanalysis.org/2024/04/24/A...
MDAnalysis Workshop June 24-25th 2024 at Arizona State University. A Saguaro cactus in the desert with flowers shaped like the MDAnalysis logo.
April 24, 2024 at 6:24 PM
mdanalysis.bsky.social
Our next keynote speaker for the #mdaUGM2024 is Dr. Francesca Stanzione, a Senior Scientist at Sosei Heptares!

Read more on the MDAnalysis blog: mdanalysis.org/2024/03/14/u...
Dr. Francesca Stanzione, Senior Scientist, Sosei Heptares. Francesca is a computational chemist with over a decade expertise in target assessment, hit identification and lead optimisation. After obtaining a Ph.D. in Biotechnology, Francesca embarked on a distinguished career path. With five years of postdoctoral fellowships Francesca’s work centered on characterising the structural and dynamical properties of complex biological systems, including proteins and protein-ligand complexes, biological membranes and biomaterials. In 2023, Francesca joined Sosei Heptares, a renowned player in the pharmaceutical industry, where she now provides invaluable computational support to a variety of drug discovery campaigns. Prior to her role at Sosei Heptares, Francesca was at the Cambridge Crystallographic Data Centre (CCDC), working closely with software developers to help the development and enhancement of computational tools for drug discovery.
March 15, 2024 at 4:31 PM
mdanalysis.bsky.social
Meet our first keynote speaker for the #mdaUGM2024: Dr. Antonia Mey, a Chancellor's Fellow at the University of Edinburgh School of Chemistry!

Read more on our blog: mdanalysis.org/2024/03/14/u...
Dr. Antonia Mey, Chancellor's Fellow, University of Edinburgh School of Chemistry. Antonia has worked on Markov State models with Frank Noe and alchemical free energy calculations with Julien Michel before starting her own research group in 2020. Her group works on computational biophysics problems using machine learning and simulations to understand protein function. She is an advocate for open-source software and diamond open access publishing models. She has contributed to pyEmma, BioSimSpace and she and her group (https://mey-research.org) are avid users of MDAnalysis.
March 15, 2024 at 4:29 PM
mdanalysis.bsky.social
Do you know some Python but want to learn about analyzing and visualizing molecular simulation data? Join us Feb 28 at 3:00 UTC for a free workshop on a basic workflow with MDAnalysis and Molecular Nodes!

Spots are limited, so make sure to apply before Feb 19: www.mdanalysis.org/2024/02/05/m...
February 5, 2024 at 4:29 PM
mdanalysis.bsky.social
Looking for some good Friday reading? Check out the amazing work Xu Hong and Egor completed during the GSoC 2023 program:

www.mdanalysis.org/2024/01/18/g...

Also, please get in touch with us if you are interested in #mentoring with MDAnalysis for the GSoC 2024 program!
January 19, 2024 at 10:00 AM
mdanalysis.bsky.social
🗓️ Save the date for #mdaUGM2024 ! 🗓️

The MDAnalysis UGM 2024 will take place August 21-23, 2024 in London, UK at King's College London, in partnership with the Thomas Young Centre! Stay tuned for updates.

www.mdanalysis.org/blog/#save-t...
January 15, 2024 at 6:08 PM