Molecular dynamics study of a lipid bilayer: Convergence, structure, and long-time dynamics

Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nosé-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such as atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence to the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in the bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made.