Mesoscale simulations have recently been developed in order to better understand the collective behaviour of dislocations and their effects on the mechanical response. Those simulations deal with dislocations discretized into segments which are allowed to move in a three-dimensional (3D) discrete network. This network is a sublattice of the original crystalline lattice network. The minimum distance between two points is defined by the annihilation distance for two edge dislocations, i.e. the minimum distance for which two edge dislocations can coexist without instantaneous collapse. The elastic theory can still be applied in the simulated volume, since the minimum distance is large compared to the dislocation core radius within which nonlinear expressions should be taken into account in the dislocation-dislocation interaction. This property allows us to use the superposition principle to enforce boundary conditions on the simulation box. This paper details the rigorous boundary conditions applied when the simulation box is supposed to be either a bulk crystal, a free standing film or a finite crystal submitted to a complex loading.