Mineralization of hydroxyapatite is a complex and highly controlled process involving interactions of biological and mineral components. Understanding the basic interactions between individual amino acids and hydroxyapatite at the (001) and (020) surfaces at pH 7 and 5 is a crucial step in understanding the mineralization process and potentially aiding in designing peptides to direct and control growth of bone allograft and biomimetic materials. In our study, a combination of steered and unrestrained molecular dynamics simulations using the CHARMM36 and Interface force field parameters are used to study the dynamic nature of hydroxyapatite as well as the binding conformations of N and C capped amino acids. The results indicate that charged amino acids have a distinctly higher affinity to the mineral surface than non-charged amino acids. Binding site preferences, conformations, and the effects of pH and surface facet on the affinities are reported, and significant differences for Arginine, Glutamic Acid, Aspartic Acid, and Lysine quantified. The trends provide valuable insight into the affinity and binding mechanism of the building blocks of larger biological structures such peptides and proteins onto hydroxyapatite surfaces. The results will be useful in designing peptides to target specific bone facets for growth or suppression as well as potentially offering the ability to target specific bone sites where infections exist.