A computer program has been implemented for simulating the electron-proton instability of a partially neutralized long proton bunch. The simulation is based on a theoretical model that considers the motions of the proton-beam centroid and macro-particles representing electrons as well as the contribution of secondary emission of electrons due to impingement of particles on the beam pipe. Preliminary results from simulating thee-pinstability in the PSR are consistent with earlier studies using the centroid model and qualitatively agree well with experimental observations. It is found that enhancement of the instability due to the electron multiplication occurs only when oscillation of the proton beam has grown to large amplitude. This simulation program can be also used to find the beam-intensity threshold for multipactoring. ©1999 American Institute of Physics.