Abstract. The article discusses the effect of substituting calcium ions Ca²⁺ in certain positions of hydroxyapatite with iron ions Fe²⁺ and Fe³⁺. It shows how to use molecular dynamics simulations with a skewed cell in periodic boundary conditions to find the density of hydroxyapatite. The obtained density values are in good agreement with known data and the results of density functional theory calculations. The article also describes the process of ion evaporation, melting, and sublimation of different hydroxyapatite samples. The molecular dynamics simulation results show significant differences in the temperatures of structural rearrangements for hydroxyapatite with Fe²⁺ and Fe³⁺ substitutions. For example, the hydroxyapatite sample with Fe²⁺ ions experiences significant structural rearrangements in the temperature range of 727–827 °C, which is consistent with the experimental data on the decomposition of cation-substituted hydroxyapatite with iron ions at temperatures around 800 °C.

 

Key words: molecular dynamics method, algorithm for searching root mean square deviations of atoms, hydroxyapatite