The large variability of biological responses to beta-TCP implants reported in the literature could possibly be related to subtle differences in the beta-TCP crystal structure. The structure contains one partially occupied site Ca(4). In order to better understand the ordering of this site, 12 pairs of unit cells with different Ca(4) site occupancies were combined in different checkerboard patterns with an average occupancy of 3. Atomistic simulations were conducted to identify the lowest energy configurations. The previously published low energy configuration is not the most stable one when considering a larger supercell. Plotting the 662 simulation outputs by lattice parameters a or c versus relative lattice energy revealed clusters of high density which are composed of configurations with predominant motifs of Ca(4) occupancy. The tools introduced in this study can be applied in future simulation studies to better explain the Ca(4) site occupancy in the beta-TCP crystal structure.