[en] The molecular dynamics method was used to simulate the conformation changes of the secondary structure of peptide molecules induced by MeV proton irradiation. The simulation results indicate that the sample's secondary structure was changed from α-helix to β-sheet gradually when the sample got energy higher than 3-5 eV from the incident ion, and the energy transfer mode has significant effect on final secondary structure of the sample. besides, the proton irradiation causes manifold final secondary structures compared with that caused by raising the sample temperature. (authors)