Ideally, the steric interactions between protein atoms and the ions in the aqueous medium are to use a repulsive potential like Lennard-Jones to prevent ions from penetrating the protein. As this approach could add a significant load to the amount of calculations, a simpler approach is chosen that treats the protein surfaces as predetermined hard wall boundaries. Many recent open source molecular biology packages have built-in facilities that determine the volume accessible to ions in a protein system. The Adaptive Poisson Boltzmann Solver (APBS) scheme has been incorporated to BioMOCA to obtain the accessible volume region and therefore partition the simulation domain into continuous regions.