Assessment of all-atom potentials for modeling membranes: molecular dynamics simulations of solid and liquid alkanes and crystals of phospholipid fragments

We present and evaluate the performance of an all-atom hydrocarbon potential for use in computer simulations of lipids. The performance is judged by comparing the results of constant pressure and temperature molecular dynamics simulations to experimental data for normal alkanes: solid octane and tricosane, and liquid butane, octane, tetradecane, and eicosane. The model exhibits good overall agreement with experimentally determined crystal structures, densities, energies, and diffusion constants, although some detailed aspects of the Liquid structure and conformational equilibria are not quantitatively reproduced. We have also checked the performance of four different all-atom models for the polar moeities of phospholipid molecules by constant pressure molecular dynamics simulations of crystals of phospholipid fragments: glycerylphosphorylcholine (GPC), cyclopentylphosphorylcholine mono hydrate (CPPC), and dilauroylglycerol (DLG). Simulations of GPC and CPPC showed that recent modifications to the phosphate parameters significantly improved the performance of the CHARMM 22 potential. The results obtained using two potentials based on the work of Stouch et al. reproduced all of the crystal structures quite well.