Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane.
Computer simulations of phospholipid membranes have been carried out by using a combined approach of molecular and stochastic dynamics and a mean field based on the Marcelja model. First, the single-chain mean field simulations of Pastor et al. [(1988) J. Chem. Phys. 89, 1112-1127] were extended to a complete dipalmitoylphosphatidylcholine molecule; a 102-ns Langevin dynamics simulation is presented and compared with experiment. Subsequently, a hexagonally packed seven-lipid array was simulated with Langevin dynamics and a mean field at the boundary and with molecular dynamics (and no mean field) in the center. This hybrid method, mean field stochastic boundary molecular dynamics, reduces bias introduced by the mean field and eliminates the need for periodic boundary conditions. As a result, simulations extending to tens of nanoseconds may be carried out by using a relatively small number of molecules to model the membrane environment. Preliminary results of a 20-ns simulation are reported here. A wide range of motions, including overall reorientation with a nanosecond decay time, is observed in both simulations, and good agreement with NMR, IR, and neutron diffraction data is found.
De Loof
H
H
Department of Biochemistry, University of Alabama, Birmingham 35294.
Harvey
S C
SC
Segrest
J P
JP
Pastor
R W
RW
D003198:Computer Simulation; D008433:Mathematics; D008954:Models, Biological; D008958:Models, Molecular; D008968:Molecular Conformation; D010743:Phospholipids / Q000737:chemistry*; D013269:Stochastic Processes
D010743:Phospholipids