Two decades of Martini

Bibliographic Details
Main Author: Marrink, Siewert J.
Publication Date: 2023
Other Authors: Monticelli, Luca, Melo, Manuel N., Alessandri, Riccardo, Tieleman, D. Peter, Souza, Paulo C.T.
Format: Other
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10362/158515
Summary: Funding Information: Work in DPTs group is supported by the Natural Sciences and Engineering Research Council (Canada). Further support came from the Canada Research Chairs program. Riccardo Alessandri is supported by the Dutch Research Council (NWO Rubicon 019.202EN.028). Luca Monticelli is supported by the French National Institute of Health and Medical Research (INSERM). Paulo C. T. Souza is supported by French National Center for Scientific Research (CNRS). Further funding of Paulo C. T. Souza and Luca Monticelli came from a research collaboration with PharmCADD. Siewert J. Marrink is supported by an Advanced Grant (COMP‐O‐CELL) from the European Research Council. Publisher Copyright: © 2022 The Authors. WIREs Computational Molecular Science published by Wiley Periodicals LLC.
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spelling Two decades of MartiniBetter beads, broader scopecoarse grainingMartini force fieldmolecular dynamicsBiochemistryComputer Science ApplicationsPhysical and Theoretical ChemistryComputational MathematicsMaterials ChemistryFunding Information: Work in DPTs group is supported by the Natural Sciences and Engineering Research Council (Canada). Further support came from the Canada Research Chairs program. Riccardo Alessandri is supported by the Dutch Research Council (NWO Rubicon 019.202EN.028). Luca Monticelli is supported by the French National Institute of Health and Medical Research (INSERM). Paulo C. T. Souza is supported by French National Center for Scientific Research (CNRS). Further funding of Paulo C. T. Souza and Luca Monticelli came from a research collaboration with PharmCADD. Siewert J. Marrink is supported by an Advanced Grant (COMP‐O‐CELL) from the European Research Council. Publisher Copyright: © 2022 The Authors. WIREs Computational Molecular Science published by Wiley Periodicals LLC.The Martini model, a coarse-grained force field for molecular dynamics simulations, has been around for nearly two decades. Originally developed for lipid-based systems by the groups of Marrink and Tieleman, the Martini model has over the years been extended as a community effort to the current level of a general-purpose force field. Apart from the obvious benefit of a reduction in computational cost, the popularity of the model is largely due to the systematic yet intuitive building-block approach that underlies the model, as well as the open nature of the development and its continuous validation. The easy implementation in the widely used Gromacs software suite has also been instrumental. Since its conception in 2002, the Martini model underwent a gradual refinement of the bead interactions and a widening scope of applications. In this review, we look back at this development, culminating with the release of the Martini 3 version in 2021. The power of the model is illustrated with key examples of recent important findings in biological and material sciences enabled with Martini, as well as examples from areas where coarse-grained resolution is essential, namely high-throughput applications, systems with large complexity, and simulations approaching the scale of whole cells. This article is categorized under: Software > Molecular Modeling Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Computational Biochemistry and Biophysics.Instituto de Tecnologia Química e Biológica António Xavier (ITQB)RUNMarrink, Siewert J.Monticelli, LucaMelo, Manuel N.Alessandri, RiccardoTieleman, D. PeterSouza, Paulo C.T.2023-09-30T22:18:15Z2023-01-012023-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/otherapplication/pdfhttp://hdl.handle.net/10362/158515eng1759-0876PURE: 72092170https://doi.org/10.1002/wcms.1620info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-05-22T18:14:49Zoai:run.unl.pt:10362/158515Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T17:45:19.924885Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Two decades of Martini
Better beads, broader scope
title Two decades of Martini
spellingShingle Two decades of Martini
Marrink, Siewert J.
coarse graining
Martini force field
molecular dynamics
Biochemistry
Computer Science Applications
Physical and Theoretical Chemistry
Computational Mathematics
Materials Chemistry
title_short Two decades of Martini
title_full Two decades of Martini
title_fullStr Two decades of Martini
title_full_unstemmed Two decades of Martini
title_sort Two decades of Martini
author Marrink, Siewert J.
author_facet Marrink, Siewert J.
Monticelli, Luca
Melo, Manuel N.
Alessandri, Riccardo
Tieleman, D. Peter
Souza, Paulo C.T.
author_role author
author2 Monticelli, Luca
Melo, Manuel N.
Alessandri, Riccardo
Tieleman, D. Peter
Souza, Paulo C.T.
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Instituto de Tecnologia Química e Biológica António Xavier (ITQB)
RUN
dc.contributor.author.fl_str_mv Marrink, Siewert J.
Monticelli, Luca
Melo, Manuel N.
Alessandri, Riccardo
Tieleman, D. Peter
Souza, Paulo C.T.
dc.subject.por.fl_str_mv coarse graining
Martini force field
molecular dynamics
Biochemistry
Computer Science Applications
Physical and Theoretical Chemistry
Computational Mathematics
Materials Chemistry
topic coarse graining
Martini force field
molecular dynamics
Biochemistry
Computer Science Applications
Physical and Theoretical Chemistry
Computational Mathematics
Materials Chemistry
description Funding Information: Work in DPTs group is supported by the Natural Sciences and Engineering Research Council (Canada). Further support came from the Canada Research Chairs program. Riccardo Alessandri is supported by the Dutch Research Council (NWO Rubicon 019.202EN.028). Luca Monticelli is supported by the French National Institute of Health and Medical Research (INSERM). Paulo C. T. Souza is supported by French National Center for Scientific Research (CNRS). Further funding of Paulo C. T. Souza and Luca Monticelli came from a research collaboration with PharmCADD. Siewert J. Marrink is supported by an Advanced Grant (COMP‐O‐CELL) from the European Research Council. Publisher Copyright: © 2022 The Authors. WIREs Computational Molecular Science published by Wiley Periodicals LLC.
publishDate 2023
dc.date.none.fl_str_mv 2023-09-30T22:18:15Z
2023-01-01
2023-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/other
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status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/158515
url http://hdl.handle.net/10362/158515
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1759-0876
PURE: 72092170
https://doi.org/10.1002/wcms.1620
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
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collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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