Publication

Dual Resolution Membrane Simulations Using Virtual Sites

Liu, Y., De Vries, A. H., Barnoud, J., Pezeshkian, W., Melcr, J. & Marrink, S. J., 14-May-2020, In : The Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical. 124, 19, p. 3944-3953 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
Pages (from-to)3944-3953
Number of pages10
JournalThe Journal of Physical Chemistry. B: Materials, Surfaces, Interfaces, & Biophysical
Volume124
Issue number19
Early online date21-Apr-2020
Publication statusPublished - 14-May-2020

    Keywords

  • MOLECULAR-DYNAMICS SIMULATIONS, COARSE-GRAINED MODEL, FORCE-FIELD, BIOMOLECULAR SYSTEMS, PHASE-SEPARATION, MARTINI, ALGORITHM, VALIDATION, POTENTIALS, SOFTWARE

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