Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions.
We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using the particle-mesh Ewald (PME) technique. All examined truncation distances (1.8-2.5 nm) lead to major effects on the bilayer properties, such as enhanced order of acyl chains together with decreased areas per lipid. The results obtained using PME, on the other hand, are consistent with experiments. These artifacts are interpreted in terms of radial distribution functions g(r) of molecules and molecular groups in the bilayer plane. Pronounced maxima or minima in g(r) appear exactly at the cutoff distance indicating that the truncation gives rise to artificial ordering between the polar phosphatidyl and choline groups of the DPPC molecules. In systems described using PME, such artificial ordering is not present.
Patra
M
M
Biophysics and Statistical Mechanics Group, Laboratory of Computational Engineering, Helsinki University of Technology, FIN-02015 HUT, Finland.
Karttunen
M
M
Hyvönen
M T
MT
Falck
E
E
Lindqvist
P
P
Vattulainen
I
I
D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry*; D016477:Artifacts; D003198:Computer Simulation; D004563:Electrochemistry / Q000379:methods*; D008051:Lipid Bilayers / Q000737:chemistry*; D046911:Macromolecular Substances; D008560:Membrane Fluidity; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012996:Solutions; D055672:Static Electricity; D013499:Surface Properties; D014867:Water / Q000737:chemistry*
D008051:Lipid Bilayers; D046911:Macromolecular Substances; D012996:Solutions; D014867:Water; D015060:1,2-Dipalmitoylphosphatidylcholine