Molecular dynamics simulations of gel (LβI) phase lipid bilayers in constant pressure and constant surface area ensembles

The results of a series of molecular dynamics simulations of the gel state of a dipalmitoylphosphatidylcholine bilayer at 293 K are described. The simulations, ranging from 40 ps to 2.5 ns, show clearly that: a flexible cell geometry is essential during equilibration; Ewald summation of electrostatics is superior to spherical cutoff methods; water exchange with the carbonyl group of chain 2 takes place on the ns time scale, while there is almost no hydration of chain 1. There is overall good agreement (D-spacing, chain tilt, fraction gauche, and area compressibility modulus) with experiment, though the surface area per lipid is slightly underestimated. The randomization of torsion 1 of chain 2 from exclusively gauche minus (as specified in the initial condition modeled from the crystal structure of a related lipid) to a mixture of $\mathrm{g+/g-}$ over the course of approximately 2 ns is a critical feature of the study. The torsional equilibration proceeded steadily when simulating at constant surface tension, but was effectively quenched by simulation at constant area. The associated presence of conformational degeneracy of this torsion, and conformational disorder in the upper region of chain 2, is most likely associated with the seemingly anomalous infrared (IR) results for gauche bonds in the upper region of the chains. It may also be a characteristic of the gel phase, and be related to the long time required for the gel to subgel transition.