MDAnalysis

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...

MDAnalysis Workshop June 24-25th 2024, Arizona State University. Stylized saguaro cactus with flowers shaped like the MDAnalysis logo.

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 at Arizona State University. A Saguaro cactus in the desert with flowers shaped like the MDAnalysis logo.

Save the date: June 24th & 25th: Joint MDAnalysis/MolSSI workshop at Arizona State University. Details to follow.

www.mdanalysis.org/2024/04/24/A...

🚨 Last call (TODAY) for abstract submissions for the #mdaUGM2024 !

Submit here: docs.google.com/forms/d/e/1F...

Read more about the user group meeting here: www.mdanalysis.org/pages/ugm2024/

Do you know Python and want to learn about analysing molecular simulations data? Join us 10 May at University College London for an MD trajectory analysis using MDAnalysis workshop!

The deadline to register is 9 April (£10, includes lunch). Read more and register: www.mdanalysis.org/2024/03/30/t...

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.

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. 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.

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...

Happy Friday! We have exciting #mdaUGM2024 updates: www.mdanalysis.org/2024/03/14/u...

1️⃣ Meet 2 of our keynote speakers: Drs. Antonia Mey and Francesca Stanzione! We will introduce them in other posts.

2️⃣ The abstract and travel bursary submission deadline has been extended to April 15, 2024.

📢 Tomorrow, March 15th is the deadline for submitting your pre-proposals to work with MDAnalysis in #GSOC 2024!

For more details, visit our blog post: www.mdanalysis.org/2024/02/27/g...