title: Effects of truncating van der Waals interactions in lipid bilayer simulations.
abstract: In membrane simulations, it is known that truncating electrostatic interactions results in artificial ordering of lipids at the truncation distance. However, less attention has been paid to the effect of truncating van der Waals (VDW) interactions. Since the VDW potential decays as r(-6), it is frequently neglected beyond a cutoff of around 1 nm. In some cases, analytical dispersion corrections appropriate for isotropic systems are applied to the pressure and the potential energy. In this work, we systematically study the effect of truncating VDW interactions at different cutoffs in 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine bilayers with the Berger force field. We show that the area per lipid decreases systematically when the VDW cutoff (r(c)) increases. This dependence persists even when dispersion corrections are applied. Since the analytical form of the dispersion correction is only appropriate for isotropic systems, we suggest that a long VDW cutoff should be used in preference over a short VDW cutoff. To determine the appropriate cutoff, we simulate liquid pentadecane with the Berger parameters and find that r(c) ≥ 1.4 nm is sufficient to reproduce the density and the heat of vaporization of pentadecane. Bilayers simulated with r(c) ≥ 1.4 nm show an improved agreement with experiments in both the form factors and the deuterium order parameters. Finally, we report that the VDW cutoff has a significant impact on the lipid flip-flop energetics and an inappropriate short VDW cutoff results in a bilayer that is prone to form water defects across the bilayer.
authors.affiliation: Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
authors.forename: Kun
authors.initials: K
authors.lastname: Huang
authors.affiliation: Department of Physics, Applied Physics and Astronomy, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
authors.forename: Angel E
authors.initials: AE
authors.lastname: García
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000031:analogs & derivatives* / Q000737:chemistry; D000473:Alkanes / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D000473:Alkanes; D008051:Lipid Bilayers; C033245:pentadecane; D015060:1,2-Dipalmitoylphosphatidylcholine; C081581:colfosceril palmitate