Pitfalls of the Martini Model

Detalhes bibliográficos
Autor(a) principal: Alessandri, Riccardo
Data de Publicação: 2019
Outros Autores: Souza, Paulo C.T., Thallmair, Sebastian, Melo, Manuel N., De Vries, Alex H., Marrink, Siewert J.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/96649
Resumo: R.A. thanks The Netherlands Organisation for Scientific Research NWO (Graduate Programme Advanced Materials, No. 022.005.006) for financial support. S.T. thanks the European Commission for financial support via a Marie Skłodowska-Curie Actions Individual Fellowship (MicroMod-PSII, grant agreement 748895).
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spelling Pitfalls of the Martini ModelComputer Science ApplicationsPhysical and Theoretical ChemistryR.A. thanks The Netherlands Organisation for Scientific Research NWO (Graduate Programme Advanced Materials, No. 022.005.006) for financial support. S.T. thanks the European Commission for financial support via a Marie Skłodowska-Curie Actions Individual Fellowship (MicroMod-PSII, grant agreement 748895).The computational and conceptual simplifications realized by coarse-grain (CG) models make them a ubiquitous tool in the current computational modeling landscape. Building block based CG models, such as the Martini model, possess the key advantage of allowing for a broad range of applications without the need to reparametrize the force field each time. However, there are certain inherent limitations to this approach, which we investigate in detail in this work. We first study the consequences of the absence of specific cross Lennard-Jones parameters between different particle sizes. We show that this lack may lead to artificially high free energy barriers in dimerization profiles. We then look at the effect of deviating too far from the standard bonded parameters, both in terms of solute partitioning behavior and solvent properties. Moreover, we show that too weak bonded force constants entail the risk of artificially inducing clustering, which has to be taken into account when designing elastic network models for proteins. These results have implications for the current use of the Martini CG model and provide clear directions for the reparametrization of the Martini model. Moreover, our findings are generally relevant for the parametrization of any other building block based force field.Instituto de Tecnologia Química e Biológica António Xavier (ITQB)RUNAlessandri, RiccardoSouza, Paulo C.T.Thallmair, SebastianMelo, Manuel N.De Vries, Alex H.Marrink, Siewert J.2020-04-22T22:34:42Z2019-10-082019-10-08T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article13application/pdfhttp://hdl.handle.net/10362/96649eng1549-9618PURE: 16765944https://doi.org/10.1021/acs.jctc.9b00473info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:44:14Zoai:run.unl.pt:10362/96649Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:38:37.538822Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Pitfalls of the Martini Model
title Pitfalls of the Martini Model
spellingShingle Pitfalls of the Martini Model
Alessandri, Riccardo
Computer Science Applications
Physical and Theoretical Chemistry
title_short Pitfalls of the Martini Model
title_full Pitfalls of the Martini Model
title_fullStr Pitfalls of the Martini Model
title_full_unstemmed Pitfalls of the Martini Model
title_sort Pitfalls of the Martini Model
author Alessandri, Riccardo
author_facet Alessandri, Riccardo
Souza, Paulo C.T.
Thallmair, Sebastian
Melo, Manuel N.
De Vries, Alex H.
Marrink, Siewert J.
author_role author
author2 Souza, Paulo C.T.
Thallmair, Sebastian
Melo, Manuel N.
De Vries, Alex H.
Marrink, Siewert J.
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 Alessandri, Riccardo
Souza, Paulo C.T.
Thallmair, Sebastian
Melo, Manuel N.
De Vries, Alex H.
Marrink, Siewert J.
dc.subject.por.fl_str_mv Computer Science Applications
Physical and Theoretical Chemistry
topic Computer Science Applications
Physical and Theoretical Chemistry
description R.A. thanks The Netherlands Organisation for Scientific Research NWO (Graduate Programme Advanced Materials, No. 022.005.006) for financial support. S.T. thanks the European Commission for financial support via a Marie Skłodowska-Curie Actions Individual Fellowship (MicroMod-PSII, grant agreement 748895).
publishDate 2019
dc.date.none.fl_str_mv 2019-10-08
2019-10-08T00:00:00Z
2020-04-22T22:34:42Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/96649
url http://hdl.handle.net/10362/96649
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1549-9618
PURE: 16765944
https://doi.org/10.1021/acs.jctc.9b00473
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 13
application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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