We present new parallel algorithms for solving the problem of many body interactions in molecular dynamics (MD). Such algorithms are essential in the simulation of irradiation effects in crystals, where the high energy of the impinging particles dictates computing with large numbers of atoms and for many time cycles. We realized the algorithms using two parallelization methods and compared their performance. Experimental results obtained on a Meiko machine demonstrate that the new algorithms exploit parallelism effectively and can be used to simulate large crystals.