Advances in computing hardware and algorithms have led to molecular dynamical models being able to model more realist cases. In this paper, we focus on a special case of molecular dynamics as a starting example. The molecular dynamical simulations that model slip-stick friction are often very large and complex, requiring a great deal of computational resources and time to run. In this paper, proper orthogonal decomposition (POD), a model reduction technique that has been successfully applied to a number of different application areas, is applied to the nanoscale slip-stick friction problem. The standard POD approach, and a modified version of the POD technique that is particularly aimed at the stick-slip problem, are presented.