We report molecular dynamics calculations of the phase transition of copper precipitates in iron. We simulate a precipitate having undergone a phase transition from a bcc structure coherent with the iron matrix to a non-coherent close packed structure, as has been observed experimentally. Analytical tools were developed to simulate cross-sectional images and diffraction patterns of the precipitates so that their structure could be analysed and results compared directly with experiment. The results of the simulations support the theory of precipitate evolution put forward by Othen et al. where the precipitate goes from the bcc to the twinned 9R crystal structure. Also, the vacancy concentration and distribution are shown to be very important to precipitate evolution and to have a large influence on the stability of bcc precipitates.