We present an efficient method for the creation of atomistic model structures of cross-linked polymer matrices. The method consists of preparation of a physical mixture of the monomer and the cross-linker molecules in the box followed by a single-step polymerization of the entire mixture. For this purpose, the simulated annealing algorithm is used to identify pairs of reacting atoms that are spatially close. The technique is used to create five structures of cross-linked epoxy as well as cross-linked epoxy-POSS (i.e., polyhedral oligomeric silsesquioxane) nanocomposite. The models so generated are characterized with respect to the density, volume-temperature behavior, and the detailed molecular structure. Our results show that incorporation of POSS particles (at 5 wt %) in the cross-linked epoxy resin leads to a weak tendency for lowering the coefficient of volume thermal expansion but does not cause a measurable change in the glass transition temperature.