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CompBioPhys

@compbiophys.bsky.social
445 followers 96 following 137 posts

News and views from the research groups of H. Grubmüller & B. de Groot @MPI-NATGöttingen, Germany, Imprint: www.mpinat.mpg.de/en/imprint

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CompBioPhys @compbiophys.bsky.social · 29/09/2026
👉 Don't miss the next @bioexcelcoe.bsky.social #Webinar with 〰️Carter! @carterjwilson.bsky.social @mpi-nat.bsky.social #GROMACS #proteins #PMX
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Martin Vögele @martinvoegele.bsky.social · 25/09/2026
New preprint: We demonstrate how to apply FEP-based ligand efficacy modeling to ion channels. #CompChem 💻:⚗️ #Science 🧪 #DrugDiscovery #IonChannel #FEP doi.org/10.64898/202...
Graphical abstract: a ligand (green) binding to an ion channel resolved in antagonist- (blue) and agonist-preferred (orange) states, with state-specific binding free energies ΔG_I and ΔG_A. The right panel shows that the free-energy difference ΔG_A − ΔG_I predicts maximal ligand response, separating agonists (orange dots) from antagonists (blue squares) via a sigmoidal fit.
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Excited to share our new preprint! 📜 Here, we used CALVADOS and ultra-CG models to show how the kinetochore establishes a robust attachment to the dynamic microtubule end. Spoiler: IDRs 🧵 1/n www.biorxiv.org/content/10.6...
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
How does the kinetochore (KT) stay attached to a microtubule (MT) that is constantly assembling and disassembling? In this work, we propose that the answer lies largely in intrinsically disordered regions that form a dynamic interface between the Dam1c ring and the MT. 2/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
In budding yeast, the KT not only stays attached to a dynamic MT, but also shows tension-dependent behavior. Tension stabilizes attachment to a disassembling MT: the stronger you pull, the stronger the attachment, much like a finger trap. Yet overall, KTs bind more strongly to growing MTs. 3/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
To understand this behavior, we simulated the complete Dam1c ring–MT complex using CALVADOS. We found that the ring binds the MT through a multivalent electrostatic interface formed mainly by intrinsically disordered regions. 4/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Because individual contacts are short-lived and constantly reform, much like in the ProTα–H1 complex, the whole interface remains highly dynamic, allowing the ring to diffuse rapidly along the MT. 5/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Then what stops it from diffusing off the tip? One argument against a diffusive ring is that it will slide right off a growing tip, which lacks large curled protofilaments (PFs) to sterically block it. We find that this dynamic interface itself creates a substantial barrier to ring escape. 6/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Even when all PFs are straight and the tip is blunt, it takes a lot of force to pull the ring off. But this force can be reduced by making the tip more ragged: a tapered shape lets the tail contacts unbind gradually instead of breaking all at once. 7/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
So what about curled PFs? They surely can block the ring from sliding. To test this, we used our previously developed ultra-CG model of MT-end dynamics. And yes, long PFs distributed symmetrically around the ring can create a high barrier to unbinding. 8/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
The catch is that realistic shortening MT tips have only a few long PFs. Using tip structures based on our previous cryo-ET data, we find that the force strongly depends on PF arrangement: when long PFs cluster together, the ring can tilt and bypass them, creating a low-barrier escape route. 9/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Putting both contributions together and accounting for the full ensemble of possible MT-tip structures, we obtain rupture forces close to experiment. The key point is that detachment is dominated by rare, weak-grip configurations rather than by the average tip. 10/n
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
This also explains the stronger attachment to growing tips: they are blunt and do not have the weak-grip configurations of shortening ends, such as tapered shapes and clustered long PFs. So the tails grip them really strongly. 11/n
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BioExcel CoE @bioexcelcoe.bsky.social · 24/09/2026
🛑 The 𝗿𝗲𝗴𝗶𝘀𝘁𝗿𝗮𝘁𝗶𝗼𝗻 𝗱𝗲𝗮𝗱𝗹𝗶𝗻𝗲 for our #workshop in Athens, Greece is tomorrow, 𝗙𝗿𝗶𝗱𝗮𝘆 𝟮𝟱𝘁𝗵 𝗦𝗲𝗽𝘁𝗲𝗺𝗯𝗲𝗿 Don't miss out and register➡️ bioexcel.eu/a9nq @ezgikaraca.bsky.social #ComputerSimulation #moleculardynamics #integrativemodelling #workflows #CryoEM
bioexcel.eu
BioExcel / EuroCC workshop on Biomolecular Simulations: Aegean Edition
Registration for this event is open Our sixth Ambassador Program workshop is jointly organised and supported by our colleagues at the National Competence Centre in Greece, the Biomedical Research Foundation, Academy of Athens and Izmir Biomedicine and Genome Center, Dokuz Eylul University. The hands-on workshop is aimed at
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CompBioPhys @compbiophys.bsky.social · 24/09/2026
Great news! 🎉 Congrats to @maxotubule.bsky.social @maksimkalutskii.bsky.social @mpi-nat.bsky.social and Birkbeck, University of London! Happy reading!! 📜
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BioExcel CoE @bioexcelcoe.bsky.social · 17/09/2026
✍ Don't forget to register for our special edition webinar happening next week, where you will get 1️⃣, 2️⃣, 3️⃣ talks from our Summer School 2026 poster prize winners! 👇
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CompBioPhys @compbiophys.bsky.social · 17/09/2026
Wir suchen Dich als #IT -Experten am @mpi-nat.bsky.social in #Göttingen 🇩🇪 für den Betrieb und den Ausbau des Linux-GPU Clusters der Abteilung Theoretische und Computergestützte Biophysik! #joboffer #job #openposition #IT-Stelle 🔗 www.mpinat.mpg.de/5292977/23-26 📩 Bewirb Dich bis 📅 18.10.2026!
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CompBioPhys @compbiophys.bsky.social · 11/09/2026
📜 We're delighted to share the latest preprint from David that suggests heuristics for more efficient non-equilibrium free energy calculations of realistic molecular systems. @arxiv.bsky.social @mpi-nat.bsky.social 🔗 Further details: arxiv.org/abs/2609.10519
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 20/08/2026
11 speakers explore research & big questions – from democracy and climate to AI, cooperation & killer asteroids: check out the programme of this year’s science series at 📚 Göttinger Literaturherbst, Oct. 2.-11.: www.literaturherbst.com/programm/wis...
René Heller, Christiane Kofri, Guido Schriever (oben, v.l.), Sonja Lorenz und Frauke Alves (unten, v.l.) stellten beim Pressegespräch am 20. August die elf Autor*innen und zehn Sachbücher der Vortragsreihe Wissenschaft beim Göttinger Literaturherbst vor.
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 10/08/2026
Many snapshots of the cancer protein p53, superimposed on top of one another and color-coded, illustrate the complex motion patterns of this intrinsically disordered protein. Some of the transient structural elements appear as “helix-like structures”. © @dszollosi.bsky.social / MPI-NAT (3/3)
Many snapshots of the cancer protein p53, superimposed on top of one another and color-coded, illustrate the complex motion patterns of this intrinsically disordered protein. Some of the transient structural elements appear as “helix-like structures”.
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 11/08/2026
🎓 From PhD to Nobel Prize: Join our PhD day for a Q&A with Nobel laureates Erwin Neher + Stefan Hell, a PhD poster session + info booths on careers, funding, startups, mental health, equal opportunities + more for early career scientits in Göttingen. 📅 Sept 4 | 📝 events.gwdg.de/event/1513/
Plakat PhD Day 2026 am MPI-NAT
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 10/08/2026
How researchers visualized, for the 1st time, how the 3D structure of cancer protein p53 changes dynamically over time – in slow motion up to ultrafast time lapse: www.mpinat.mpg.de/5304698/pr_2... lead researchers: Helmut Grubmüller (head of @compbiophys.bsky.social) + Christian Griesinger (2/3)
mpinat.mpg.de
Cancer protein p53 observed in action
Researchers unveil dynamic 3D structures of cancer protein p53, revealing unexpected order and complexity in its function.
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 10/08/2026
Looks unorganized to you? It isn’t. Indeed, you are looking at fixed 3D structures of the cancer protein p53. It can adopt at least 50 different 3D structures and is much more ordered than previously thought! 🎥© @dszollosi.bsky.social l / MPI-NAT @compbiophys.bsky.social (1/3)
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Max Bonomi @bonomimax.bsky.social · 22/07/2026
Fantastic opportunity at @pasteur.fr in Spyros’ brand new lab, especially if you like protein design 🎉
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CompBioPhys @compbiophys.bsky.social · 16/07/2026
We are hiring an #IT expert! Interested to join our department @mpi-nat.bsky.social in #Göttingen 🇩🇪 as Hardware Operations Technician (IT-Systemtechniker*in)? Please apply! 📩 #joboffer #job #openposition 🔗 www.mpinat.mpg.de/5292977/23-26 📅 Don't miss the application deadline: August 23, 2026
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CompBioPhys @compbiophys.bsky.social · 22/06/2026
Just in case you missed it... 👉 📽️#webinar @bioexcelcoe.bsky.social @lindorfflarsen.bsky.social
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CompBioPhys @compbiophys.bsky.social · 19/06/2026
🎉 We are delighted to see our latest #publication online introducing a #MM model that reconciles the decade-long bi-site versus tri-site controversy, showing that both pathways contribute depending on #ATP concentration. #F1-ATPase @springernature.com 🔗 www.nature.com/articles/s41...
nature.com
A minimal chemo-mechanical Markov model for rotary catalysis of F1-ATPase - Nature Communications
F1-ATPase is a rotary motor protein essential for cellular energy transduction. Here the authors develop a thermodynamically consistent Markov model that quantitatively matches experimental data and r...
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BioExcel CoE @bioexcelcoe.bsky.social · 19/06/2026
Don't forget to register for our hands-on #workshop focused on the use of #GROMACS, #PMX and #BioBB 🗓️ 8-9 September 2026 🌍 Gliwice, Poland 🛑 Registration deadline 30 June 2026 ➡️ bioexcel.eu/a0ov #ComputerSimulation #moleculardynamics #workflows
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BioExcel CoE @bioexcelcoe.bsky.social · 20/05/2026
Experience the BioExcel demo booth at the upcoming conference on Advances in Biomolecular Simulations ✅ Live demos of core codes #GROMACS #HADDOCK #PMX #BioBB ✅ Support from experts ✅ ..and more! ✍️𝘙𝘦𝘨𝘪𝘴𝘵𝘳𝘢𝘵𝘪𝘰𝘯: bioexcel.eu/hzr0
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CompBioPhys @compbiophys.bsky.social · 28/04/2026
👉 Don't miss your opportunity to join the upcoming @bioexcelcoe.bsky.social #conference in Brno 🇨🇿 in September! #ComputerSimulation #MD More details:🔗https://bioexcel.eu/events/3rd-bioexcel-conference-on-advances-in-biomolecular-simulations/
bioexcel.eu
3rd BioExcel Conference on Advances in Biomolecular Simulations
Registration for the 3rd BioExcel Conference on Advances in Biomolecular Simulations is now open! Date: 27 – 30 September 2026 Venue: Brno, Czech Republic Important dates: 19 January 2026: Registrat...
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Phil Biggin @philbiggin.bsky.social · 06/05/2026
Congratulations to Bjarne Feddersen for his work on benchmarking umbrella sampling workflows for PMF calculations of membrane permeation! Systematic work that provides guidance on how to approach these to minimise compute resource. @oxfordbiochemistry.bsky.social. pubs.acs.org/doi/10.1021/...
pubs.acs.org
Umbrella Sampling Workflows for Fast-Converging PMF Calculations without Artificial WHAM Constraints
Umbrella sampling is a powerful tool to investigate the underlying free-energy landscapes that govern the permeation properties of small molecules through complex lipid bilayers. However, obtaining co...
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CompBioPhys @compbiophys.bsky.social · 04/05/2026
We are hiring an #IT expert! Interested to join our department @mpi-nat.bsky.social in #Göttingen 🇩🇪 as #SysAdmin or #HPC infrastructure manager? Please apply! 📩 #joboffer #job #openposition 🔗 www.mpinat.mpg.de/5256103/13-2... 📅 Don't miss the application deadline: May 17, 2026
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Michal Kolář @mhko.bsky.social · 30/04/2026
We open up to two Junior PI positions at UCT Prague, Czechia @vschtpraha.bsky.social. Broadly defined chemistry-related projects will be considered. A support from any department must be negotiated prior application. Feel free to contact me for further info or visit www.vscht.cz/research/dag....
vscht.cz
Starting grants – Institutional Research Support - University of Chemistry and Technology, Prague
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CompBioPhys @compbiophys.bsky.social · 04/05/2026
We are happy to share our latest publication with you that just appeared in J. #Proteome Res. @pubs.acs.org pubs.acs.org/doi/10.1021/... 🙏 Many thanks for the great collaboration with our colleagues @mpibiochem.bsky.social in Martinsried! #proteomics #IMS #MD #peptides
pubs.acs.org
Bimodal Peptide Collision Cross Section Distribution Reflects Two Stable Conformations in the Gas Phase
Recent high-throughput applications to shotgun proteomics have shown great benefits of coupling ion mobility spectrometry (IMS) to mass spectrometry. IMS adds a separation dimension by differentiating...
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CompBioPhys @compbiophys.bsky.social · 28/04/2026
👉 Don't miss your opportunity to join the upcoming @bioexcelcoe.bsky.social #conference in Brno 🇨🇿 in September! #ComputerSimulation #MD More details:🔗https://bioexcel.eu/events/3rd-bioexcel-conference-on-advances-in-biomolecular-simulations/
bioexcel.eu
3rd BioExcel Conference on Advances in Biomolecular Simulations
Registration for the 3rd BioExcel Conference on Advances in Biomolecular Simulations is now open! Date: 27 – 30 September 2026 Venue: Brno, Czech Republic Important dates: 19 January 2026: Registrat...
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 23/04/2026
Imagine being 11 years old, walking into a lab, putting on your lab coat 🥼 and gloves, and getting started. Waiting for you: a microscope 🔬, real samples, and lots of questions. Today is Future Day – and this is what the morning looks like for the school students visiting the MPI-NAT 🙂!
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CompBioPhys @compbiophys.bsky.social · 28/04/2026
It was indeed great fun to participate in this annual event! Thanks to our guests and orga team @mpi-nat.bsky.social for a this wunderful experience. Hope to see you at some point again.. Maybe as junior researcher in our lab! 😀 #FutureDay
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 21/04/2026
HPC trifft Forschung 💻🔬 – wir suchen dich! Du willst nicht nur Systeme verwalten, sondern Wissenschaft möglich machen? Dann komm als IT-Systemadministrator*in / HPC-Infrastruktur-Manager*in in unsere Abteilung @compbiophys.bsky.social. Alles weitere erfährst du hier: www.mpinat.mpg.de/13-26
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BioExcel CoE @bioexcelcoe.bsky.social · 13/04/2026
Join our #webinar tomorrow "Multiscale simulation of biomembranes: shape, structure and cellular function" 🗓️ 14 April 2026, 15:00 CET ✍️ bioexcel.eu/y50u #ComputerSimulation #moleculardynamics @weria-lab.bsky.social
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CompBioPhys @compbiophys.bsky.social · 01/04/2026
We are looking for an #IT expert to join our department @mpi-nat.bsky.social in #Göttingen 🇩🇪 as #SysAdmin or #HPC infrastructure manager! More details in our current job offer 🔗 www.mpinat.mpg.de/5238050/13-2... Is it you?🧐 Please apply! 📩 #joboffer #job #openposition
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CompBioPhys @compbiophys.bsky.social · 06/02/2026
🧐 You are a physicist or chemist who wants to reveal how life works at the molecular level? 🤓 You know how to combine computer power and theory to solve biological problems? ❤️ You just love doing science? 👉 Send us your application! 🔗 Current job adverts www.mpinat.mpg.de/grubmueller
Job advert for MD related research projects in the department of theoretical and computational biophysics @mpi-nat.bsky.social
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CompBioPhys @compbiophys.bsky.social · 31/03/2026
👉 #webinar @bioexcelcoe.bsky.social on characterising dynamic #protein interfaces with DynaPIN #software #today
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CompBioPhys @compbiophys.bsky.social · 24/03/2026
👉 Another excellent @bioexcelcoe.bsky.social #webinar today!
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 20/03/2026
Save the date 📅: @horizonsmolbio.bsky.social Symposium 2026 Look forward to an international conference from Sep 7 to 10 at our institute – you can expect exciting scientific presentations from fields such as cell biology, structural biology, bioinformatics, neuroscience, genomics, and immunology. 👇
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FAU Erlangen-Nbg @fau.de · 02/02/2026
Impfstoffe und andere Medikamente werden zum Schutz oft in kleinen Fetttröpfchen verpackt, den sogenannten Lipid-Nanopartikeln. So werden sie von den Zellen aufgenommen und entlassen erst dann ihre Fracht. Um diesen Prozess zu optimieren, haben FAU-Forschende den Vorgang am Computer simuliert. (1/2)
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BioExcel CoE @bioexcelcoe.bsky.social · 03/03/2026
Following our "What's new in GROMACS 2026" webinar today we have another webinar in 2 weeks where we will focus on #GROMACS performance 🗓️ 17 March 2026, 15:00 CET ✍️ bioexcel.eu/oryy #webinar #moleculardynamics @gromacs.bsky.social
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CompBioPhys @compbiophys.bsky.social · 03/03/2026
Don't miss the @bioexcelcoe.bsky.social #webinar TODAY! 😲 What's new in GROMACS 2026.0 🧐
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CompBioPhys @compbiophys.bsky.social · 03/03/2026
🙂 Happy to share our contribution to improving the understanding of #ionchannels! In this review, the authors attempt to elucidate how the modulator pocket contributes to #K2P channel activation. #TREK1 #MD #C-type inactivation #ML335 #review @wojciechkopec.bsky.social 👉 doi.org/10.1080/1933...
doi.org
One pocket to activate them all (?): Efforts on understanding the modulator pocket in K2P channels
The modulator pocket is a cryptic site discovered in the TREK1 (K2P2.1) K2P channel. This pocket, located close to the selectivity filter, accommodates agonists that enhance the channel’s activity....
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CompBioPhys @compbiophys.bsky.social · 26/02/2026
🎉Just appeared online in #JCTC @pubs.acs.org "Improving Conformational Ensembles of Folded #Proteins in #GōMartini" @maksimkalutskii.bsky.social @maxotubule.bsky.social @carterjwilson.bsky.social pubs.acs.org/doi/10.1021/...
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CompBioPhys @compbiophys.bsky.social · 20/02/2026
👉 Don't miss your chance to get the latest news about GROMACS 2026 and join the @bioexcelcoe.bsky.social #webinar with Vedran, Lukas and Berk on March 3! @gromacs.bsky.social #MD #moleculardynamics
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