It was noticed for some time ago that molecular dynamics simulations of phospholipid bilayers using the standard CHARMM27 force field, under condition of zero surface tension, results in unrealistically low area per lipid and in too ordered bilayer structure. We modified the CHARMM force field for phospholipids, by reparametrizing the partial atom charges on the basis of high-level ab-initio calculations, and introducing a scaling factor for the 1-4 electrostatic interactions. Calculations of partial atom charges were made for ensemble of conformations of the whole lipid head group including esters, which were taken from the molecular dynamics trajectory. The resulting partial charges were then averaged over the conformations. This modification, taken together with the use of scaling factor for the 1-4 electrostatic interactions, reproducing experimentally known ratio of trans-gauche conformations in the lipid tails, and with the use of flexible SPC water model having correct dielectric permittivity, results in a lipid bilayer structure which is in perfect agreement with different experimental data, such as area per lipid, electron density profile, structure factor, and the NMR order parameters.
Equilibrated structure: 98 DMPC lipids + 2700 (fSPC) waters:
DMPC_98.start
The DMPC structure-parameter file: dmpc.mmol