Molecular dynamics of the Yukawa system, the system of particles interacting via the Yukawa or the screened Coulomb potential, are formulated for various statistical ensembles and external conditions. The Yukawa potential smoothly interpolates the long-range Coulomb and the short-range interactions by adjusting a single parameter, the screening length. In order to reduce the effect of boundaries, the periodic boundary conditions are imposed and the deformations of the fundamental vectors of periodicity are taken into account. Ewald-type expressions for interaction energy, force, and kinematic pressure are given explicitly.