Molecular dynamics simulation of phospholipid bilayer membrane

Starting from the crystal structure of l-α-dimyristoylphosphatidylcholine (DMPC), liquid-crystalline bilayer membrane in its thermal equilibrium state was generated by molecular dynamics simulations. Two bilayer membranes were generated using different sets of force fields. System 1 contains 6167 united atoms (56 DMPC molecules and 1197 water molecules), and the calculation was carried out over 10 ns starting from the crystal structure. Initial structure of System 2 was constructed based on the thermally equilibrated System 1, but the system size was enlarged, and an all-atom force field was applied (112 DMPC molecules and 3016 water molecules). Various values of surface tension were incorporated to examine its effects on the nature of simulated bilayers, and to find proper values of surface tension to each system. Analyses of both membranes revealed that their structural parameters, including order parameter of the alkyl chains, surface area per lipid, number of gauche conformation per chain, agree with each other and experimental estimates.