METHODS, SYSTEMS, AND COMPUTER PROGRAM PRODUCTS FOR SIMULATING BIOMEMBRANES USING COARSE GRAIN MODELS

摘要

A coarse grain model that mimics a lipid molecule, such as dimyristoylphosphatidylcholine (DMPC), is used to simulate self-assembly of a lamellar bilayer starting from a disordered configuration. The coarse grain model is orders of magnitude less demanding of CPU time compared to all-atom models. An initial bilayer-like structure is generated from a disordered configuration of the coarse grain models using a Monte Carlo simulation. The initial bilayer-like structure is refined using a molecular dynamics simulation. For relatively small systems, the molecular dynamics simulation can be performed under constant volume or constant pressure conditions. For larger systems, the molecular dynamics simulation is preferably performed under constant pressure conditions.