A classical interatomic potential model has been developed for systems consisting of hydrogen, carbon and nitrogen atoms. By using the new potential model, molecular dynamics simulations of low energy beam injections are carried out for an organic polymer substrate. Dose dependence of the net sputtering yields of a poly(1,4-phenylene) substrate by radical beam injections is obtained with the injection energy of 25 eV. Simulation results suggest that injected carbon or nitrogen atoms contribute to the formation of possible passivation layers.