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 lightweight armor development, gas storage, n-type thermoelectrics. In this work, we introduce a modeling framework to obtain basic interatomic pair potentials and to simulate the basic mechanical behavior of these materials with molecular dynamics. We use a combination of density functional theory (DFT), molecular dynamics (MD), 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. DFT methods are used to generate energetics data for multiple configurations of these materials. Interatomic potentials are obtained by inversion methods, which further optimized using MD to reproduce dynamic behavior such as mean-square displacements obtained from the quantum harmonic approximation at the MD level.