Dual Resolution Membrane Simulations Using Virtual Sites

Journal article
Multi-scale
Methods
Vesicles
Lipid membranes
Author

Yang Liu, Alex H De Vries, Jonathan Barnoud, Weria Pezeshkian, Josef Melcr, Siewert J Marrink

Doi

https://doi.org/10.1021/acs.jpcb.0c01842

Citation (APA 7)

Liu, Y., De Vries, A. H., Barnoud, J., Pezeshkian, W., Melcr, J., & Marrink, S. J. (2020). Dual resolution membrane simulations using virtual sites. The Journal of Physical Chemistry B, 124(19), 3944-3953.

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.