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Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG
[Image: see text] After two decades of continued development of the Martini coarse-grained force field (CG FF), further refinment of the already rather accurate Martini lipid models has become a demanding task that could benefit from integrative data-driven methods. Automatic approaches are increasi...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10302490/ https://www.ncbi.nlm.nih.gov/pubmed/37279107 http://dx.doi.org/10.1021/acs.jcim.3c00530 |
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author | Empereur-mot, Charly Pedersen, Kasper B. Capelli, Riccardo Crippa, Martina Caruso, Cristina Perrone, Mattia Souza, Paulo C. T. Marrink, Siewert J. Pavan, Giovanni M. |
author_facet | Empereur-mot, Charly Pedersen, Kasper B. Capelli, Riccardo Crippa, Martina Caruso, Cristina Perrone, Mattia Souza, Paulo C. T. Marrink, Siewert J. Pavan, Giovanni M. |
author_sort | Empereur-mot, Charly |
collection | PubMed |
description | [Image: see text] After two decades of continued development of the Martini coarse-grained force field (CG FF), further refinment of the already rather accurate Martini lipid models has become a demanding task that could benefit from integrative data-driven methods. Automatic approaches are increasingly used in the development of accurate molecular models, but they typically make use of specifically designed interaction potentials that transfer poorly to molecular systems or conditions different than those used for model calibration. As a proof of concept, here, we employ SwarmCG, an automatic multiobjective optimization approach facilitating the development of lipid force fields, to refine specifically the bonded interaction parameters in building blocks of lipid models within the framework of the general Martini CG FF. As targets of the optimization procedure, we employ both experimental observables (top-down references: area per lipid and bilayer thickness) and all-atom molecular dynamics simulations (bottom-up reference), which respectively inform on the supra-molecular structure of the lipid bilayer systems and on their submolecular dynamics. In our training sets, we simulate at different temperatures in the liquid and gel phases up to 11 homogeneous lamellar bilayers composed of phosphatidylcholine lipids spanning various tail lengths and degrees of (un)saturation. We explore different CG representations of the molecules and evaluate improvements a posteriori using additional simulation temperatures and a portion of the phase diagram of a DOPC/DPPC mixture. Successfully optimizing up to ∼80 model parameters within still limited computational budgets, we show that this protocol allows the obtainment of improved transferable Martini lipid models. In particular, the results of this study demonstrate how a fine-tuning of the representation and parameters of the models may improve their accuracy and how automatic approaches, such as SwarmCG, may be very useful to this end. |
format | Online Article Text |
id | pubmed-10302490 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-103024902023-06-29 Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG Empereur-mot, Charly Pedersen, Kasper B. Capelli, Riccardo Crippa, Martina Caruso, Cristina Perrone, Mattia Souza, Paulo C. T. Marrink, Siewert J. Pavan, Giovanni M. J Chem Inf Model [Image: see text] After two decades of continued development of the Martini coarse-grained force field (CG FF), further refinment of the already rather accurate Martini lipid models has become a demanding task that could benefit from integrative data-driven methods. Automatic approaches are increasingly used in the development of accurate molecular models, but they typically make use of specifically designed interaction potentials that transfer poorly to molecular systems or conditions different than those used for model calibration. As a proof of concept, here, we employ SwarmCG, an automatic multiobjective optimization approach facilitating the development of lipid force fields, to refine specifically the bonded interaction parameters in building blocks of lipid models within the framework of the general Martini CG FF. As targets of the optimization procedure, we employ both experimental observables (top-down references: area per lipid and bilayer thickness) and all-atom molecular dynamics simulations (bottom-up reference), which respectively inform on the supra-molecular structure of the lipid bilayer systems and on their submolecular dynamics. In our training sets, we simulate at different temperatures in the liquid and gel phases up to 11 homogeneous lamellar bilayers composed of phosphatidylcholine lipids spanning various tail lengths and degrees of (un)saturation. We explore different CG representations of the molecules and evaluate improvements a posteriori using additional simulation temperatures and a portion of the phase diagram of a DOPC/DPPC mixture. Successfully optimizing up to ∼80 model parameters within still limited computational budgets, we show that this protocol allows the obtainment of improved transferable Martini lipid models. In particular, the results of this study demonstrate how a fine-tuning of the representation and parameters of the models may improve their accuracy and how automatic approaches, such as SwarmCG, may be very useful to this end. American Chemical Society 2023-06-06 /pmc/articles/PMC10302490/ /pubmed/37279107 http://dx.doi.org/10.1021/acs.jcim.3c00530 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Empereur-mot, Charly Pedersen, Kasper B. Capelli, Riccardo Crippa, Martina Caruso, Cristina Perrone, Mattia Souza, Paulo C. T. Marrink, Siewert J. Pavan, Giovanni M. Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG |
title | Automatic Optimization
of Lipid Models in the Martini
Force Field Using SwarmCG |
title_full | Automatic Optimization
of Lipid Models in the Martini
Force Field Using SwarmCG |
title_fullStr | Automatic Optimization
of Lipid Models in the Martini
Force Field Using SwarmCG |
title_full_unstemmed | Automatic Optimization
of Lipid Models in the Martini
Force Field Using SwarmCG |
title_short | Automatic Optimization
of Lipid Models in the Martini
Force Field Using SwarmCG |
title_sort | automatic optimization
of lipid models in the martini
force field using swarmcg |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10302490/ https://www.ncbi.nlm.nih.gov/pubmed/37279107 http://dx.doi.org/10.1021/acs.jcim.3c00530 |
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