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🔬 Coarse-Grained Modeling @ ACS Fall 2025 — Program Out Now! 🚀 📍 Washington DC | Aug 17–21 - Wed, Aug 20 AM: LNPs — nucleic acid delivery → viral entry simulations - Wed, Aug 20 PM: Proteins & multiscale modeling - Thu, Aug 21 AM: Methods & industry

New preprint: “When lipids embrace RNA” www.biorxiv.org/content/10.6... Using multiscale simulations (🍸 #Martini + constant-pH MD), we show that: • Local pKa ≠ global pKa • Endosomal escape is limited by persistent protonation. #LNP #MolecularDynamics

Our collaborative work "The #Martini3 #Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior" is now published in #ACSCentralScience! 🎉 📄 Read: pubs.acs.org/doi/10.1021/... 💾 GitHub: github.com/Martini-Forc... #MolecularDynamics #Biophysics #Simulations #Lipids

Thanks to sponsors: Google Cloud & MolCube! 📄 Full program: acs.digitellinc.com/live/35/page... #ACSFall2025 #ComputationalChemistry #CoarseGrainedModeling

Very happy to see our recent work featured on the cover of the Journal of Chemical Theory and Computation 🎉 A long journey with many people involved — grateful to everyone who helped make this happen. Paper: pubs.acs.org/doi/10.1021/... @pubs.acs.org #MyACSCover #JCTC #Martini3

Lipid membranes are central to cellular life. Complementing experiments, computational modeling has been essential in unraveling complex lipid-biomolecule interactions, crucial in both academia and industry. The Martini model, a coarse-grained force field for efficient molecular dynamics simulations, is widely used to study membrane phenomena but has faced limitations, particularly in capturing realistic lipid phase behavior. Here, we present refined Martini 3 lipid models with a mapping scheme that distinguishes lipid tails that differ by just two carbon atoms, enhancing the structural resolution and thermodynamic accuracy of model membrane systems including ternary mixtures. The expanded Martini lipid library includes thousands of models, enabling simulations of complex and biologically relevant systems. These advancements establish Martini as a robust platform for lipid-based simulations across diverse fields.

Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇

Our collective work with @tbereau.bsky.social and @pauloctsouza.bsky.social labs to automatically parametrize CG models of small molecules is now published in JCTC! Nice Christmas present for 1st author @szczukam.bsky.social and all the coauthors! pubs.acs.org/doi/full/10....

Coarse-grained molecular dynamics simulations, such as those performed with the recently parametrized Martini 3 force field, simplify molecular models and enable the study of larger systems over longer time scales. With this new implementation, Martini 3 allows more bead types and sizes, becoming more amenable to studying dynamical phenomena involving small molecules such as protein–ligand interactions and membrane permeation. However, while solutions existed to automatically model small molecules using the previous iteration of the Martini force field, there is no simple way to generate such molecules for Martini 3 yet. Here, we introduce Auto-MartiniM3, an advanced and updated version of the Auto-Martini program designed to automate the coarse-graining of small molecules to be used with the Martini 3 force field. We validated our approach by modeling 81 simple molecules from the Martini Database and comparing their structural and thermodynamic properties with those obtained from models designed by Martini experts. Additionally, we assessed the behavior of Auto-MartiniM3-generated models by calculating solute translocation and free energy across lipid bilayers. We also evaluated more complex molecules such as caffeine by testing its binding to the adenosine A2A receptor. Finally, our results from deploying Auto-MartiniM3 on a large data set of molecular fragments demonstrate that this program can become a tool of choice for fast, high-throughput creation of coarse-grained models of small molecules, offering a good balance between automation and accuracy. Auto-MartiniM3 source code is freely available at https://github.com/Martini-Force-Field-Initiative/Automartini_M3.

🚀 New preprint out! "Fast Parameterization of #Martini3 Models for Fragments and Small Molecules" is now on #bioRxiv 👉 doi.org/10.1101/2025... #AutoMartiniM3 – tool for automated #CG modeling. With @matthchavent.bsky.social, @tbereau.bsky.social and others. #CoarseGraining #MD #DrugDiscovery

Looking forward to #acsfall2025! Hoping to finally meet in person the colleagues I’ve long admired at the @acscomp.bsky.social reception Sunday as well. 😄🍸

🚀 Sponsorship opportunities still available 📍 Lyon, France | 14–16 October 2026 Registration opening soon. Stay tuned for further announcements! #CGML2026 #MachineLearning #MolecularModeling #CoarseGrained #DrugDiscovery #Formulations #MaterialsScience