ArticleBiophysical journal2023
An implementation of the Martini coarse-grained force field in OpenMM.
Article in Biophysical journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- SMartini: automated small molecule parametrization for Martini 3 force field.bioRxiv : the preprint server for biology · 2026Article
- Integrative structural modelling reveals the human Mic60-Mic19 subcomplex as a diffusion barrier in mitochondria.Nature communications · 2026Article
- Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics.Scientific reports · 2026Article
- Structural Modulation and Binding of HLA-DQ8 by Cysteine-to-Serine Mutated Insulin Peptide: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2026Article
- Integrating NMR Restraints into Coarse-Grained Simulations: Toward Accurate Conformational Ensembles of Complex Protein Systems.Journal of the American Chemical Society · 2026Article
- Compartment-guided assembly of large-scale molecular models with Bentopy.Protein science : a publication of the Protein Society · 2026Article
- GōMartini 3: From large conformational changes in proteins to environmental bias corrections.Nature communications · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- Martini 3 OliGo̅mers: A Scalable Approach for Multimers and Fibrils in GROMACS.Journal of chemical theory and computation · 2024Article
- [Research progress of coarse-grained molecular dynamics in drug carrier materials].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2023Review
- Biophysics at the dawn of exascale computers.Biophysical journal · 2023Article
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Authors and funding
6 authors.
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Abstract
We describe a complete implementation of Martini 2 and Martini 3 in the OpenMM molecular dynamics software package. Martini is a widely used coarse-grained force field with applications in biomolecular simulation, materials, and broader areas of chemistry. It is implemented as a force field but makes extensive use of facilities unique to the GROMACS software, including virtual sites and bonded terms that are not commonly used in standard atomistic force fields. OpenMM is a flexible molecular dynamics package widely used for methods development and is competitive in speed on GPUs with other commonly used packages. OpenMM has facilities to easily implement new force field terms, external forces and fields, and other nonstandard features, which we use to implement all force field terms used in Martini 2 and Martini 3. This allows Martini simulations, starting with GROMACS topology files that are processed by custom scripts, with all the added flexibility of OpenMM. We provide a GitHub repository with test cases, compare accuracy and performance between GROMACS and OpenMM, and discuss the limitations of our implementation in terms of direct comparison with GROMACS. We describe a use case that implements the Modeling Employing Limited Data method to apply experimental constraints in a Martini simulation to efficiently determine the structure of a protein complex. We also discuss issues and a potential solution with the Martini 2 topology for cholesterol.
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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.