Molecular origin of friction is related to the dissipation of the molecular motion energy responses to the external field produced by the sliding motion. Molecular dynamics simulations are suitable method to describe the process. In this article we review a history of molecular dynamics simulation related to tribology and show the “tribo-molecular dynamics” established in 1990s. If the major energy dissipation mode is restricted to the molecular motion in the vicinity of the surface, it is boundary lubrication and fully described by the simulation. In usual case of hydrodynamic lubrication or solid lubrication, however, molecular simulation can not describe the full process due to the large correlation length or low frequency vibration of the system. The understanding of the restriction is important in practical use of the method.