Molecular Dynamics Simulations of Phospholipid Bilayers: Influence of Artificial Periodicity, System Size, and Simulation Time Export

@article{citeulike:2391692, abstract = {Abstract: This article investigates the convergence of structural and dynamical properties with system size and with time in molecular dynamics simulations of solvated phospholipid bilayers performed at constant volume under periodic boundary conditions using lattice-sum electrostatics. The electron density profile across the bilayer, the carbon-deuterium order parameters, and the surface tension are shown to be converged for a bilayer containing 36 lipids per leaflet and simulated over a period of 3-4 ns. Reasonable estimates for these properties can already be obtained from a system containing 16 lipids per leaflet. The convergence limit of 36 lipids per leaflet and the investigation of the correlation between lipid headgroup dipoles suggest a correlation length of about 3-5 nm in the lateral directions for a hydrated DPPC bilayer in the liquid-crystalline phase. Although these (relatively small) system sizes and (relatively short) time scales appear sufficient to obtain converged collective structural properties at constant volume, two restrictions should be kept in mind: (i) the relaxation times associated with the motion of individual lipids may be much longer and (ii) simulated properties converge significantly faster under constant volume conditions as compared to constant pressure conditions. Therefore, an accurate assessment of the dynamical properties of the system or of the relaxation of the bilayer under constant pressure conditions may require longer simulation time scales.}, address = {Laboratory of Physical Chemistry, ETH, ETH H\"{o}nggerberg, CH-8093 Z\"{u}rich, Switzerland}, author = {Devries, A. H. and Chandrasekhar, I. and Vangunsteren, W. F. and Hunenberger, P. H.}, citeulike-article-id = {2391692}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/jp0507952}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/jp0507952}, day = {16}, doi = {10.1021/jp0507952}, journal = {J. Phys. Chem. B}, keywords = {artifacts}, month = {June}, number = {23}, pages = {11643--11652}, posted-at = {2008-02-18 00:16:18}, priority = {2}, title = {Molecular Dynamics Simulations of Phospholipid Bilayers: Influence of Artificial Periodicity, System Size, and Simulation Time}, url = {http://dx.doi.org/10.1021/jp0507952}, volume = {109}, year = {2005} }

TY - JOUR ID - citeulike:2391692 L3 - citeulike-article-id:2391692 N2 - Abstract: This article investigates the convergence of structural and dynamical properties with system size and with time in molecular dynamics simulations of solvated phospholipid bilayers performed at constant volume under periodic boundary conditions using lattice-sum electrostatics. The electron density profile across the bilayer, the carbon-deuterium order parameters, and the surface tension are shown to be converged for a bilayer containing 36 lipids per leaflet and simulated over a period of 3-4 ns. Reasonable estimates for these properties can already be obtained from a system containing 16 lipids per leaflet. The convergence limit of 36 lipids per leaflet and the investigation of the correlation between lipid headgroup dipoles suggest a correlation length of about 3-5 nm in the lateral directions for a hydrated DPPC bilayer in the liquid-crystalline phase. Although these (relatively small) system sizes and (relatively short) time scales appear sufficient to obtain converged collective structural properties at constant volume, two restrictions should be kept in mind: (i) the relaxation times associated with the motion of individual lipids may be much longer and (ii) simulated properties converge significantly faster under constant volume conditions as compared to constant pressure conditions. Therefore, an accurate assessment of the dynamical properties of the system or of the relaxation of the bilayer under constant pressure conditions may require longer simulation time scales. IS - 23 JF - J. Phys. Chem. B AD - Laboratory of Physical Chemistry, ETH, ETH Hönggerberg, CH-8093 Zürich, Switzerland EP - 11652 TI - Molecular Dynamics Simulations of Phospholipid Bilayers: Influence of Artificial Periodicity, System Size, and Simulation Time VL - 109 SP - 11643 KW - artifacts AU - Devries, AH AU - Chandrasekhar, I AU - Vangunsteren, WF AU - Hunenberger, PH PY - 2005/06/16/ UR - http://dx.doi.org/10.1021/jp0507952 ER -