Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters

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Abstract
We compared molecular dynamics simulations of a bilayer of 128 fully hydrated phospholipid (DPPC) molecules, using different parameters and macroscopic boundary conditions. The same system was studied under constant pressure, constant volume, and constant surface tension boundary conditions, with two different sets of charges, the single point charge (SPC) and extended single point charge (SPC/E) water model and two different sets of Lennard‐Jones parameters for the interaction between water and methyl/methylene. Some selected properties of the resulting bilayer systems are compared to each other, previous simulations, and experimental data. It is concluded that in relatively high water concentration it is possible to use ab initio derived charges with constant pressure boundary conditions. The SPC water model gives a larger area per head group and a broader interface than the SPC/E model. Increasing the repulsion between water oxygens and CH2/CH3 groups has a large effect on the width of the interface and the area per head group. There is little difference between simulations with constant pressure and constant surface tension. The use of constant volume, using a reasonable estimate for the initial box dimensions, easily introduces artefacts.