Molecular dynamics (MD) simulations, in which materials are modelled on super-computers at the level of their interacting molecules, have become an invaluable tool for studying complex systems on microscopic scales. Many problems in condensed matter physics and chemistry, which have otherwise eluded experimental and theoretical analysis, have been resolved with MD techniques. For three decades, most applications of MD focused on equilibrium properties of solids, liquids, and other condensed systems. Recently, the availability of supercomputers has led to a proliferation of exciting studies involving inhomogeneous, non-equilibrium systems. New applications include studies of fluid dynamics, atomic force microscopy, micro-indentation and ‘stick–slip’ phenomena.