Silica nanoparticles (NPs) embedded in atactic polystyrene (PS) are simulated using coarse-grained (CG) potentials obtained via iterative Boltzmann inversion (IBI). The potentials are parametrized and validated on polystyrene of 2 kDa (i.e., chains containing 20 monomers). It is shown that the CG potentials are transferable between different systems. The structure of the polymer chains is strongly influenced by the NP. Layering, chain expansion, and preferential orientation of segments as well as of entire chains are found. The extent of the structural perturbation depends on the details of the system : bare NPs vs NPs grafted with PS chains, grafting density (0, 0.5, and 1 chains/nm(2)), length of the grafted chains (2 and 8 kDa), and the matrix chains (2-20 kDa). For example, there is a change in the swelling state for the grafted corona (8 kDa, 1 chains/nm(2)), when the matrix polymer is changed from 2 to > 8 kDa. This phenomenon, sometimes called "wet brush to dry brush transition", is in good agreement with neutron scattering investigations. Another example is the behavior of the radius of gyration, of free polymer chains close to the NP. Short chains expand compared to the bulk, whereas chains whose unperturbed radius of gyration is larger than that of the NP contract.