We studied the effect of the semiclassical molecular initial ground state configuration of the nucleus on the neutron spectra for p+Al, Fe, and Zr at 1.2 GeV by using an improved ultrarelativistic quantum molecular dynamics (ImUrQMD) model. Compared to the standard UrQMD version, it incorporates: (i) Pauli potential, (ii) a medium modified NN→NΔ angular distribution, and (iii) a statistical multifragmentation decay model as an afterburner. It is shown that the slow evaporated, cascade, and quasielastic (inelastic) peaks of neutrons are all sensitive to different initialization procedures. Therefore, the implementation of a proper semiclassical ground state initialization in the ImUrQMD model is of importance for the description of all the neutron spectra in proton-induced reactions at intermediate energies (≈1GeV).