Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase

We have constructed and simulated a membrane-water system which consists of 200 molecules of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine forming a rectangular patch of a bilayer and of 5483 water molecules covering the head groups on each side of the bilayer. The total number of atoms is approximately 27 000. The lateral dimensions of the bilayer are 85 A×100 A, and the distance between the bilayer surfaces as given by the average phosphorus to phosphorus distance is 35 A. The thickness of each water layer is up to 15 A. In all, we simulated 263 ps of the dynamics of the system. To prevent system disintegration, atoms within 5 A from the surface were harmonically restrained and treated by Langevin dynamics, forming a stochastic boundary