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Dual Resolution Membrane Simulations Using Virtual Sites.
Liu, Yang; De Vries, Alex H; Barnoud, Jonathan; Pezeshkian, Weria; Melcr, Josef; Marrink, Siewert J.
Afiliação
  • Liu Y; Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands.
  • De Vries AH; Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands.
  • Barnoud J; Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands.
  • Pezeshkian W; Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands.
  • Melcr J; Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands.
  • Marrink SJ; Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, 9747 AG Groningen, The Netherlands.
J Phys Chem B ; 124(19): 3944-3953, 2020 05 14.
Article em En | MEDLINE | ID: mdl-32314586
All-atomistic (AA) and coarse-grain (CG) simulations have been successfully applied to investigate a broad range of biomolecular processes. However, the accessible time and length scales of AA simulation are limited and the specific molecular details of CG simulation are simplified. Here, we propose a virtual site (VS) based hybrid scheme that can concurrently couple AA and CG resolutions in a single membrane simulation, mitigating the shortcomings of either representation. With some adjustments to make the AA and CG force fields compatible, we demonstrate that lipid bilayer properties are well kept in our hybrid approach. Our VS hybrid method was also applied to simulate a small lipid vesicle, with the inner leaflet and interior solvent represented in AA, and the outer leaflet together with exterior solvent at the CG level. Our multiscale method opens the way to investigate biomembrane properties at increased computational efficiency, in particular applications involving large solvent filled regions.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Simulação de Dinâmica Molecular / Bicamadas Lipídicas Idioma: En Ano de publicação: 2020 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Simulação de Dinâmica Molecular / Bicamadas Lipídicas Idioma: En Ano de publicação: 2020 Tipo de documento: Article