Molecular dynamics (MD) simulations have been used to study calcium phosphate formation regulated by collagen in solution. In this study, a collagen-like peptide molecule has been mixed with different types of ions for simulations of the early stage of biomineralization. We have compared one system containing calcium ions, and hydrogen phosphate ions to the other system containing calcium ions, phosphate ions and hydroxy ions in a water box containing a peptide molecule (1CAG) in the center. After the simulations, the radical distance function and coordination number profiles show that calcium ions and phosphate ions attract each other and form stable clusters in both systems studied. The hydroxy ions are attracted by calcium ions and the distance between them is close to that in hydroxyapatite, which is considered to play important roles in the formation of hydroxyapatite. The current results provide a useful approach to study the scenario of mineralizing collagen using MD methods.