We have developed a method that reduces the CPU time required in molecular dynamics simulations of ion bombardment processes. This method is based on the selective integration of the particles of the system depending on their energy. Low energy particles are integrated less frequently than the high energy ones. In order to test our scheme we have carried out simulations of Ar+ bombardment of Si(100) at 300 K. Using this method gain factors up to 5.9 in computation speed have been achieved. The accuracy of the results was satisfactory in terms of total energy conservation and of the description of the individual trajectories of the atoms along the simulation.