Alkaline earth hexaborides are thermoelectric materials with unique thermophysical properties that have a broad variety of applications with great potential for new uses in fields such as light-weight armor development, gas storage, and n-type thermoelectrics. In this work, we introduce a modeling framework to simulate the basic mechanical behavior of these materials with molecular dynamics. We use a combination of density functional theory, molecular dynamics, and optimization methods to produce a set of interatomic potentials which can describe accurately the equilibrium energetics and mean-square displacements of atoms within these bulk hexaborides. The model works particularly well for hexaborides with large cations.