Molecular dynamics simulations of cyclic siloxane-based liquid crystals offer new insights into the conformational flexibility of these materials. Interdigitation between the cholesteryl-4′-allyloxybenzoate and biphenyl-4′-allyloxybenzoate mesogens pendant on the cyclic siloxane ring is observed in the simulated structures. All molecular models considered viz. disc, cone, and cylinder, display a large conformational flexibility, which is important regarding the liquid crystalline phase behavior. The disc molecular model exhibits the largest flexibility as indicated by mean dihedral angles and their range for certain principal torsions, evaluated from the molecular dynamics simulations. Results from the dynamics simulations of cylinder molecular pairs indicate a significant amount of conformational flexibility in the siloxane rings. The degree of interdigitation between mesogens is dependent on the flexibility of the siloxane rings, as shown by calculations for a fixed ring system resulting in less interdigitation, also reflected in calculated X-ray scattering sections along the starting molecular direction. Weaker molecular transforms were observed for the non-fixed system due to a lack of boundary conditions. In general, the qualitative agreement of the starting structure's reflections and those shown by the experimental data is encouraging.