We have used molecular simulations to study the properties of nanocomposites formed by the chemical incorporation of polyhedral oligomeric silsesquioxane (POSS) particles in the cross-linked epoxy network. The particular POSS molecule chosen—glycidyloxypropyl-heptaphenyl POSS—can form only one bond with the cross-linker and thus was present as a dangling unit in the network. Four epoxy-POSS nanocomposites containing different fractions (up to 30 mass/%) of POSS particles were studied in this work. Well-relaxed atomistic model structures of the nanocomposites were created and then molecular dynamics simulations were used to characterize the density, glass transition temperature (Tg), and the coefficient of volume thermal expansion (CVTE) of the systems. In addition to the effect of nanoparticle loading, the effect of nanoparticle chemistry on the nanocomposite properties was also characterized by comparing these results with our previous results (Lin and Khare, Macromolecules 42:4319–4327, 2009) on neat cross-linked epoxy and a nanocomposite containing a POSS nanoparticle that formed eight bonds with the cross-linked network. Our results showed that incorporation of these monofunctional POSS particles into cross-linked epoxy does not cause a measurable change in its density, glass transition temperature, or the CVTE. Furthermore, simulation results were used to characterize the aggregation of POSS particles in the system. The nanofiller particles in systems containing 11, 20, and 30 mass/% POSS were found to form small clusters. The cluster-size distribution of nanoparticles was also characterized for these systems.