Lipid bilayers: the effect of force field on ordering and dynamics

Poger, David and Mark, Alan E. (2012) Lipid bilayers: the effect of force field on ordering and dynamics. Journal of Chemical Theory and Computation, 8 11: 4807-4817. doi:10.1021/ct300675z

Author Poger, David
Mark, Alan E.
Title Lipid bilayers: the effect of force field on ordering and dynamics
Journal name Journal of Chemical Theory and Computation   Check publisher's open access policy
ISSN 1549-9618
Publication date 2012-11-13
Sub-type Article (original research)
DOI 10.1021/ct300675z
Volume 8
Issue 11
Start page 4807
End page 4817
Total pages 11
Place of publication Washington, DC, United States
Publisher American Chemical Society
Collection year 2013
Language eng
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.
Keyword Fluorescence correlation spectroscopy
Lateral diffusion-coefficients
Elastic neutron-scattering
Particle mesh ewald
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2013 Collection
School of Chemistry and Molecular Biosciences
Institute for Molecular Bioscience - Publications
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