title: Lipid Bilayers: The Effect of Force Field on Ordering and Dynamics.
abstract: The sensitivity of the structure and dynamics of a fully hydrated pure bilayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in molecular dynamics simulations to changes in force-field and simulation parameters has been assessed. Three related force fields (the Gromos 54A7 force field, a Gromos 53A6-derived parameter set and a variant of the Berger parameters) in combination with either particle-mesh Ewald (PME) or a reaction field (RF) were compared. Structural properties such as the area per lipid, carbon-deuterium order parameters, electron density profile and bilayer thicknesses, are reproduced by all the parameter sets within the uncertainty of the available experimental data. However, there are clear differences in the ordering of the glycerol backbone and choline headgroup, and the orientation of the headgroup dipole. In some cases, the degree of ordering was reminiscent of a liquid-ordered phase. It is also shown that, although the lateral diffusion of the lipids in the plane of the bilayer is often used to validate lipid force fields, because of the uncertainty in the experimental measurements and the fact that the lateral diffusion is dependent on the choice of the simulation conditions, it should not be employed as a measure of quality. Finally, the simulations show that the effect of small changes in force-field parameters on the structure and dynamics of a bilayer is more significant than the treatment of the long-range electrostatic interactions using RF or PME. Overall, the Gromos 54A7 best reproduced the range of experimental data examined.
authors.affiliation: The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane QLD 4072, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Poger
authors.affiliation: The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane QLD 4072, Australia.|The University of Queensland, Institute for Molecular Bioscience, Brisbane QLD 4072, Australia.
authors.forename: Alan E
authors.initials: AE
authors.lastname: Mark