Paper Citing NAMD - Abstract
Chowdhary, Janamejaya; Harder, Edward; Lopes, Pedro E. M.; Huang, Lei; MacKerell, Alexander D., Jr.; Roux, Benoit
A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids
JOURNAL OF PHYSICAL CHEMISTRY B, 117:9142-9160, AUG 8 2013
A polarizable force field of saturated phosphatidylcholine-containing lipids based on the classical Drude oscillator model is optimized and used in molecular dynamics simulations of bilayer and monolayer membranes. The hierarchical parametrization strategy involves the optimization of parameters for small molecules representative of lipid functional groups, followed by their application in larger model compounds and full lipids. The polar headgroup is based on molecular ions tetramethyl ammonium and dimethyl phosphate, the esterified glycerol backbone is based on methyl acetate, and the aliphatic lipid hydrocarbon tails are based on linear alkanes. Parameters, optimized to best represent a collection of gas and liquid properties for these compounds, are assembled into a complete model of dipalmitoylphosphatidylcholine (DPPC) lipids that is tested against the experimental properties of bilayer and monolayer membranes. The polarizable model yields average structural properties that are in broad accord with experimental data. The area per lipid of the model is 60 angstrom(2), slightly smaller than the experimental value of 63 angstrom(2). The order parameters from nuclear magnetic resonance deuterium quadrupolar splitting measures, the electron density profile, and the monolayer dipole potential are in reasonable agreement with experimental data, and with the nonpolarizable CHARMM C36 lipid force field.
