We discuss the use of molecular dynamics simulation methods to study disordering and ion implantation in silicon. We discuss the simulation methodology and introduce the interatomic potential employed, with a critical discussion of its applicability. We show that in silicon the displacement cascade results in a distinct primary state of damage dominated by large pockets of highly unrelaxed amorphous-like disordered silicon. The amorphous volume produced for 5 keV Si on Si cascades contains approximate to 1000 atoms, corresponding to an energy cost of approximately 10 eV/atom. Replacement collision sequences are found to be very short in silicon and as a result, very few point defects appear as a consequence of the displacement cascade. We show that upon annealing of the damage microstructure at high temperature, the amorphous pockets recrystallize and result in the freezing-in in the lattice of vacancies, SIAs and their clusters. We discuss the effect of the ion mass on defect production and amorphization, and present results on the temperature dependence of the damage as well on the stability of the damage clusters for boron and arsenic cascades.