We present a discussion of the periodic-boundary-induced strain that is necessarily present in simulations of interfaces between materials with differing lattice structures. We propose a simple, systematic method of minimizing such strain, which effectively eliminates perturbations imposed by the periodic boundaries. A sequence is formulated that characterizes the degree of strain present. This sequence is used in several examples to determine the optimal choice of periodic cell dimensions that minimize the periodic-boundary-induced strain. We show that the method is easily generalized to any interface structure.