A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field.
The performance of the GROMOS96 parameter set 45A3 developed for aliphatic alkanes is tested on a bilayer of dipalmitoylphosphatidylcholine (DPPC) in water in the liquid-crystalline L(alpha) phase. Variants of the force-field parameter set as well as different sets of simulation conditions or simulation parameter sets are evaluated. In the case of the force-field parameters, the van der Waals constants for the non-bonded interaction of the ester carbonyl carbon and the partial charges and charge group definition of the phosphatidylcholine head group are examined. On the methodological side, different cut-off distances for the non-bonded interactions, use of a reaction-field force due to long-range electrostatic interactions, the frequency of removal of the centre of mass motion and the strength of the coupling of the pressure of the system to the pressure bath are tested. The area per lipid, as a measure of structure, the order parameters of the chain carbons, as a measure of membrane fluidity, and the translational diffusion of the lipids in the plane of the bilayer are calculated and compared with experimental values. An optimal set of simulation parameters for which the GROMOS96 parameter set 45A3 yields a head group area, chain order parameters and a lateral diffusion coefficient in accordance with the experimental data is listed.
Chandrasekhar
Indira
I
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH-Hoenggerberg, 8093, Zurich, Switzerland. indira@igc.phys.chem.ethz.ch
Kastenholz
Mika
M
Lins
Roberto D
RD
Oostenbrink
Chris
C
Schuler
Lukas D
LD
Tieleman
D Peter
DP
van Gunsteren
Wilfred F
WF
D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry* / Q000592:standards; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods / Q000592:standards*; D004563:Electrochemistry / Q000379:methods* / Q000592:standards*; D004574:Electromagnetic Fields; D018499:Linear Energy Transfer; D008051:Lipid Bilayers / Q000737:chemistry* / Q000592:standards; D008055:Lipids / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation / Q000528:radiation effects; D009038:Motion; D012016:Reference Values; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D055672:Static Electricity; D013314:Stress, Mechanical
D008051:Lipid Bilayers; D008055:Lipids; D015060:1,2-Dipalmitoylphosphatidylcholine