We present molecular dynamics simulations of atomic mixing over a Si/SiO2 heterostructure interface, induced by focused Ne + and broad Si + ion-beam irradiations, using a speed-up scheme that significantly reduces the relaxation time of the cascading recoils. To assess the qualitative reliance of the chosen method, two different potential models for Si-O, Si-Si, and O-O interactions were used: the Stillinger-Weber like Watanabe-Samela potential and the Tersoff-like Munetoh potential. Furthermore, the molecular dynamics simulations were assessed by simulating a similar case, at a total fluence of 1 × 10 15 cm −2 , with the binary collision approximation. The same general atomic density profile distributions were achieved with both models, however, the binary collision approach showed shallower penetration of Si into the SiO2 layer. Coordination analysis of the molecular dynamics results provides strong evidence that ion mixing at high fluences leads to coordination defects, that will affect the electronic properties of the structures unless removed with annealing.