Dual Resolution Membrane Simulations Using Virtual Sites
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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.
In: Journal of Physical Chemistry B, Vol. 124, No. 19, 14.05.2020, p. 3944-3953.Research output: Contribution to journal › Journal article › Research › peer-review
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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