Dual Resolution Membrane Simulations Using Virtual Sites

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Standard

Dual Resolution Membrane Simulations Using Virtual Sites. / Liu, Yang; De Vries, Alex H.; Barnoud, Jonathan; Pezeshkian, Weria; Melcr, Josef; Marrink, Siewert J.

I: Journal of Physical Chemistry B, Bind 124, Nr. 19, 14.05.2020, s. 3944-3953.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Liu, Y, De Vries, AH, Barnoud, J, Pezeshkian, W, Melcr, J & Marrink, SJ 2020, 'Dual Resolution Membrane Simulations Using Virtual Sites', Journal of Physical Chemistry B, bind 124, nr. 19, s. 3944-3953. https://doi.org/10.1021/acs.jpcb.0c01842

APA

Liu, Y., De Vries, A. H., Barnoud, J., Pezeshkian, W., Melcr, J., & Marrink, S. J. (2020). Dual Resolution Membrane Simulations Using Virtual Sites. Journal of Physical Chemistry B, 124(19), 3944-3953. https://doi.org/10.1021/acs.jpcb.0c01842

Vancouver

Liu Y, De Vries AH, Barnoud J, Pezeshkian W, Melcr J, Marrink SJ. Dual Resolution Membrane Simulations Using Virtual Sites. Journal of Physical Chemistry B. 2020 maj 14;124(19):3944-3953. https://doi.org/10.1021/acs.jpcb.0c01842

Author

Liu, Yang ; De Vries, Alex H. ; Barnoud, Jonathan ; Pezeshkian, Weria ; Melcr, Josef ; Marrink, Siewert J. / Dual Resolution Membrane Simulations Using Virtual Sites. I: Journal of Physical Chemistry B. 2020 ; Bind 124, Nr. 19. s. 3944-3953.

Bibtex

@article{8c7f3d2eb2094960b6ae8f0ecdf780e6,
title = "Dual Resolution Membrane Simulations Using Virtual Sites",
abstract = "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.",
keywords = "MOLECULAR-DYNAMICS SIMULATIONS, COARSE-GRAINED MODEL, FORCE-FIELD, BIOMOLECULAR SYSTEMS, PHASE-SEPARATION, MARTINI, ALGORITHM, VALIDATION, POTENTIALS, SOFTWARE",
author = "Yang Liu and {De Vries}, {Alex H.} and Jonathan Barnoud and Weria Pezeshkian and Josef Melcr and Marrink, {Siewert J.}",
year = "2020",
month = may,
day = "14",
doi = "10.1021/acs.jpcb.0c01842",
language = "English",
volume = "124",
pages = "3944--3953",
journal = "Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "19",

}

RIS

TY - JOUR

T1 - Dual Resolution Membrane Simulations Using Virtual Sites

AU - Liu, Yang

AU - De Vries, Alex H.

AU - Barnoud, Jonathan

AU - Pezeshkian, Weria

AU - Melcr, Josef

AU - Marrink, Siewert J.

PY - 2020/5/14

Y1 - 2020/5/14

N2 - 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.

AB - 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.

KW - MOLECULAR-DYNAMICS SIMULATIONS

KW - COARSE-GRAINED MODEL

KW - FORCE-FIELD

KW - BIOMOLECULAR SYSTEMS

KW - PHASE-SEPARATION

KW - MARTINI

KW - ALGORITHM

KW - VALIDATION

KW - POTENTIALS

KW - SOFTWARE

U2 - 10.1021/acs.jpcb.0c01842

DO - 10.1021/acs.jpcb.0c01842

M3 - Journal article

VL - 124

SP - 3944

EP - 3953

JO - Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical

JF - Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical

SN - 1520-6106

IS - 19

ER -

ID: 316753471