Martini 3: A general purpose force field for coarse-grained molecular dynamics
Open accessAbstract
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers.
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Martini 3 offers an improved framework for CG MD simulations with over 800 different bead types and a recalibrated interaction matrix.
“With over 800 different bead types and a recalibrated interaction matrix, Martini 3 offers an improved framework for CG MD simulations (Souza et al., 2021).”
From Molecular dynamics simulation of an entire cell (2023) · cites this paper as Souza et al., 2021
The Results sections on bead re-parametrization and new bead types describe a fully revised interaction matrix and an expanded set of bead types, supporting the description of Martini 3 as an improved CG simulation framework. They do not substantiate the specific claim that it has over 800 different bead types; searches for that number and for a total bead-type count found no supporting passage in our copy. Page numbers were not available. (LLM, conf=0.88)
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- [74]Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP & de Vries AH The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 111, 7812– 7824 (2007). 17569554
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“With over 800 different bead types and a recalibrated interaction matrix, Martini 3 offers an improved framework for CG MD simulations (Souza et al., 2021).”
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Self-citationLipid scrambling is a general feature of protein insertases
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Conjugating Ligands to an Equilibrated Nanoparticle Protein Corona Enables Cell Targeting in Serum
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Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders
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Self-citationSchmitt, S., Fleckenstein, F., Hasse, H., & Stephan, S. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c07997 · Cited by 48 · see citing works
Gasdermin-A3 pore formation propagates along variable pathways
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Self-citationCoarse-Grained Modeling of Ion-Containing Polymers
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Structural basis of dimerization of chemokine receptors CCR5 and CXCR4
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- Authors
- Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., Kroon, P. C., Melcr, J., Nieto, V., Corradi, V., Khan, H. M., Domański, J., Javanainen, M., Martinez-Seara, H., Reuter, N., Best, R. B., Vattulainen, I., Monticelli, L., Periole, X., Tieleman, D. P., de Vries, A. H., & Marrink, S. J.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- University of Groningen (NL)
- University of Calgary (CA)
- National Institutes of Health (US)
- Tampere University (FI)
- University of Bergen (NO)
- University of Helsinki (FI)
- Corresponding author
- Souza, Paulo C. T.
- Marrink, Siewert J.
- ORCID
- Souza, Paulo C. T.
- Alessandri, Riccardo
- Barnoud, Jonathan
- Thallmair, Sebastian
- Faustino, Ignacio
- Grünewald, Fabian
- Patmanidis, Ilias
- Abdizadeh, Haleh
- Bruininks, Bart M. H.
- Wassenaar, Tsjerk A.
- Kroon, Peter C.
- Melcr, Josef
- Nieto, Vincent
- Corradi, Valentina
- Khan, Hanif M.
- Domański, Jan
- Javanainen, Matti
- Martinez-Seara, Hector
- Reuter, Nathalie
- Best, Robert B.
- Vattulainen, Ilpo
- Monticelli, Luca
- Tieleman, D. Peter
- Marrink, Siewert J.
- Venue
- Nature Methods
- Published
- 2021-03-29
- Volume
- 18
- Issue
- 4
- Pages
- 382-388
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC12554258
- OpenAlex
- W3148042916
- Cited by
- 1,551
- References
- 92
- Citations by year
- 2026: 370 · 2025: 392 · 2024: 298 · 2023: 270 · 2022: 146 · 2021: 73 · 2019: 1 · 2012: 1
- FWCI
- 117.73
- Type
- journal article
- Language
- en
- Open access
- green
- research.rug.nl
- Licence
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- HAL (submittedVersion, other-oa)
- Työväentutkimus Vuosikirja (submittedVersion)
- Lirias (KU Leuven) (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion, other-oa)
- Explore Bristol Research (submittedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Funders
- Agence Nationale de la Recherche (ANR-17-CE11-0003)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (022.005.006)
- National Institutes of Health (Z99 DK999999)
- Engineering and Physical Sciences Research Council (EP/P021123/1)
- National Institute of Diabetes and Digestive and Kidney Diseases (ZIADK075104)
- Topics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Keywords
- Martini 3 force field, coarse-grained molecular dynamics, hydrogen bonding, electronic polarizability, oil-water partitioning, miscibility, protein-protein interaction, protein-lipid interactions, ionic liquids, biomolecular simulation
- MeSH terms
- Hydrogen Bonding, Lipid Bilayers, Thermodynamics, Molecular Dynamics Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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