ArticleThe journal of physical chemistry. B2024
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 293 papers.
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Who cites it
293 citing papers in PubMed.
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- Cysteine Thioaldehydes: Photolytic Generation, Reactivity, and Biological Implications.Angewandte Chemie (International ed. in English) · 2026Article
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- SMartini: automated small molecule parametrization for Martini 3 force field.bioRxiv : the preprint server for biology · 2026Article
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- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Parameterization of the CHARMM force field for divalent cations (Ca2+/Be2+) binding to anionic lipids with isothermal titration calorimetry.The Journal of chemical physics · 2026Article
- Integrative structural modelling reveals the human Mic60-Mic19 subcomplex as a diffusion barrier in mitochondria.Nature communications · 2026Article
- Structural basis of stepwise G protein activation by the viral chemokine receptor US28.bioRxiv : the preprint server for biology · 2026Article
- Accelerated OH Oxidation of Methyl Chloride via Surface Accumulation at the Air-Water Interface.ACS physical chemistry Au · 2026Article
- CaMKII generates actin bundle morphology and mechanics distinct from canonical bivalent cross-linkers.bioRxiv : the preprint server for biology · 2026Article
- Article
- Insights into fibrinogen mechanics under cyclic high-strain loading.Biophysical journal · 2026Article
- Dynamic states of an MHC class I molecule during peptide exchange.Nature communications · 2026Article
- Enabling Biomolecular Simulations with Neural Network Potentials in GROMACS.Journal of chemical theory and computation · 2026Article
- Upcycling Vegetable Waste Into Functional Food Ingredients via Synergistic Microbial Engineering and Artificial Intelligence.Comprehensive reviews in food science and food safety · 2026Review
- Agonist-specific conformational dynamics at the βBritish journal of pharmacology · 2026Article
233 more citing papers are in PubMed but not listed here.
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Authors and funding
25 authors.
Funding
Abstract
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features in simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations with only a modest increase in cost.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.