We have used molecular dynamics (MD) to study the room temperature bulk phase behavior of a cyclic siloxane with a pentamethylcyclosiloxane core and biphenyl-4-allyloxybenzoate Mesogens (BCS). This Material exhibits thermotropic liquid crystalline behavior above 120 °C. Bonded and non-bonded interactions were considered and a Molecular Mechanics force field was used to model the structural anisotropy of the siloxane Molecules. Molecular clusters with and without periodic boundary conditions (pbc) were studied to investigate the effect of the finite system size on the time evolution of the molecular structure. The precise nature of the boundary conditions was found to be significant and simulations that exclude pbc were better able to model the molecular system. It was found that molecular shapes associated with low energy conformations were not cylindrically symmetric but more splayed like. An approximate measure of the shape of the mesogens was obtained by describing ellipsoids around the Mesogens, and estimating the molecular length, breadth, and width from the principal axes of the ellipsoids. The orientational order was then calculated by defining the molecular axis to be along the major principal axis.