Experimental and theoretical studies have suggested that cholesterol is not randomly distributed in the fluid-state lipid bilayer but forms nanoscale domains, and a variety of structures have been proposed including rafts, regular or maze arrays, complexes, and superlattices. In this study, we have used Molecular Dynamics (MD) simulations to investigate the effects of the molecular organization of lipids and water in bilayers of cholesterol and 1-palmitoyl-2-oleoyl-phosphatidylcholine/1,2-dioleoyl- phosphatidylethanolamine (cholesterol/POPC/PE). Based on replicate independent MD simulations for superlattice or random bilayer, statistically significant differences were observed in the lipid structural and chemical parameters, suggesting increased stability of the superlattice structure.