Proton diffusion in Y- and Zn-doped BaZrO3 has been studied by performing molecular dynamics (MD) simulations, where the forces acting on atoms have been computed by the density functional theory (DFT). Special attention has been paid for the dopant effect on the proton conduction. The atomic configuration of 338 atoms obtained by the simulations has been verified by infrared absorption spectroscopy and neutron and synchrotron X-ray total scattering techniques. It is found from the DFT-based MD simulation that protons tend to get localized around Zn but not Y in significant amounts even at elevated temperature. Such a trapping is also indicated by change in the infrared absorption spectra by temperature, and the atomic configuration optimized by the DFT is consistent with that refined by the reverse Monte Carlo simulation using the Bragg reflections and structure factors. From DFT calculations, it can be concluded that the differences in the effective charges between Zr and the dopants explain the reason for the strong proton trapping by Zn.