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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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“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
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Citations
Cites
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Bussi, G., Donadio, D., & Parrinello, M. (2007) · The Journal of Chemical Physics · doi:10.1063/1.2408420 · Cited by 18,327
Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
Verlet, L. (1967) · Physical Review · doi:10.1103/physrev.159.98 · Cited by 9,900
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
Marrink, . J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp071097f · Cited by 5,641
Self-citationThe MARTINI Coarse-Grained Force Field: Extension to Proteins
Monticelli, L., Kandasamy, S. K., Périole, X., Larson, R. G., Tieleman, D. P., & Marrink, . J. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct700324x · Cited by 2,521
Self-citationCoarse Grained Model for Semiquantitative Lipid Simulations
Marrink, S. J., de Vries, A. H., & Mark, A. E. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp036508g · Cited by 2,257
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Joseph, J. A., Reinhardt, A., Aguirre, A., Chew, P. Y., Russell, K. O., Espinosa, J. R., Garaizar, A., & Collepardo‐Guevara, R. (2021) · Nature Computational Science · doi:10.1038/s43588-021-00155-3 · Cited by 379
Piersimoni, L., Kastritis, P. L., Arlt, C., & Sinz, A. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00786 · Cited by 327
Bottom-up Coarse-Graining: Principles and Perspectives
Jin, J., Pak, A. J., Durumeric, A. E. P., Loose, T. D., & Voth, G. A. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00643 · Cited by 321
Two decades of Martini: Better beads, broader scope
Marrink, S. J., Monticelli, L., Melo, M. N., Alessandri, R., Tieleman, D. P., & Souza, P. C. T. (2023) · WIREs Computational Molecular Science · doi:10.1002/wcms.1620 · Cited by 255
Self-citationFrallicciardi, J., Melcr, J., Siginou, P., Marrink, . J., & Poolman, B. (2022) · Nature Communications · doi:10.1038/s41467-022-29272-x · Cited by 275
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Metadata
- 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
- 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
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