Manipulation of metal nanoparticles using atomic force microscope is a promising new technique for probing tribological properties at the nanoscale. In spite of some advancements in experimental investigations, there is no unambiguous theoretical treatment of processes accompanying the movement of metallic nanoislands adsorbed on a flat surface and additional research is required. In this paper, we describe computer experiments based on classical molecular dynamics in which the behavior of silver and nickel nanoparticles interacting with a graphene sheet and sheared with constant force is studied. Frictional force acting on the nanoislands is measured as a function of their size. It is shown that its average value grows approximately linearly with contact area, and slopes of linear fits are close to the experimentally observable ones. The dependence of the friction force value and of the shape of the measured friction curves on the type of metal atom is revealed and its possible reasons originating from atomistic background are discussed.