This chapter gives a tutorial introduction to the molecular dynamics (MD) technique as a first-principle description of classical many-particle dynamics. The goal is to provide practical insight into the current status of theoretical dusty plasma research as well as to present the necessary ingredients for a successful MD simulation in one place. As typical examples of the application of MD, we concentrate on two directions of current research interest: (1) the structural properties of spherical dust crystals in traps and (2) the transport properties such as diffusion of liquid unconfined, infinite dust systems.