Molecular dynamics simulation of a dense model bilayer of chain molecules with fixed head groups

Molecular dynamics (MD) simulations have been performed on a model bilayer of 48 chain molecules with fixed head groups and periodic boundary conditions in the lateral direction. The effects of packing density and temperature on the extent of spatial and temporal correlations in the ensemble have been studied by analyzing the trajectories from the MD simulations. Quantities such as order parameters, number density contours, trans–gauche statistics and structure factors are evaluated as a function of distance from the plane containing the constrained head groups. The ensemble having the smallest area of 20.625 Å2/molecule can be characterized as having three dimensional order, even at high temperatures, with a few gauche defects. Decreasing the packing density of the chains results in the increase of the number of gauche defects, especially at the chain extremities along with a decrease in the extent of spatial and temporal correlations. Interestingly, shorter interchain spacings are evident in the middle of the layer which can be attributed to clusters of chains lying alongside less dense domains. At temperatures lower than 300 K, the ensemble having the largest area of 26.125 Å2/molecule reveals a rather complex interplay between chains wherein the lateral arrangement of the methylene units across the layer is transient and varies as a function of distance from the plane of the head groups. At temperatures higher than 300 K, thermal motion increases chain separation which effectively suppresses cluster formation.