Molecular dynamics simulation and experimental validation by X-ray data of hydroxyapatite crystalline structures

Computer simulations have provide information about structural and dynamic properties of hydroxyapatite (HAp). However, the accuracy of simulated HAp in the description of experimental crystalline structures is not evaluated in many of theoretical studies. Here, molecular dynamics (MD) simulations of HAp in the isobaric-isothermal (NPT) ensemble are carried out using LAMMPS at temperature of 298 K and pressure of 1 atm. We evaluate the quality of two sets of force field parameters by comparison between simulated and experimental unit-cell geometry and powder X-ray diffraction (XRD) patterns. Presence of calcium vacancies is taken into account in the simulations in order to reproduce a non-stoichiometric HAp synthesized in our lab. By using the number of vacancies determined from X-ray fluorescence (XRF) results, we observe great similarity between experimental and simulated diffraction patterns and unit-cell parameters as well as in the atom positions inside the unit cell. Significant structural modifications are identified when an excessive number of calcium atoms was removed, which emphasizes the importance of considering reliable experimental data. We encourage the use of this experimental validation methodology to demonstrate the quality of any simulated crystalline structure.