A computer-implemented method for simulating a polymer material comprising a polymer, a filler and a modifying agent for increasing the affinity of the polymer to the filler is disclosed. In order to make a relaxation calculation of filler models and modified polymer models in a short period of time, a pair of filler models are defined by a pair of parallelly-opposed wall surfaces of a virtual space in which the modified polymer models are disposed, and a molecular dynamics calculation is performed.