Molecular dynamics simulation is emerging with recent advent of high-performance computers. This paper addresses an application of molecular dynamics simulation to calculation of stress intensity factors (SIF) of a material using a three-dimensional molecular model. Since the popular molecular models such as Lennard-­Jones model fails to compute behaviors of materials correctly, in this paper the embedded atomic model (EAM) was utilized. A copper plate with a single edge crack is considered to calculate SIFs in opening mode. More than ten thousand of molecules were used for the simulation and due to a large amount of com­putation, a super computer CRAY C90 was employed. The results show good agreement with the theoret­ical SIF values.