Y-doped BaZrO3 is a promising proton conductor for intermediate temperature solid oxide fuel cells. In this work, a combination of static DFT calculations and DFT based molecular dynamics (DFT-MD) was used to study proton conduction in such a material. Geometry optimisations of 100 structures with a 12.5% dopant concentration allowed us to identify a clear correlation between the bending of the metal-oxygen-metal angle and the energies of the simulated cells. Depending on the type of bending, two configurations, designated as inwards bending and outwards bending, were defined. The results demonstrate that a larger bending decreases the energy and that the lowest energies are observed for structures combining inwards bending with protons being close to the dopant atoms. These lowest energy structures are the ones with the strongest hydrogen bonds. DFT-MD simulations in cells with different yttrium distributions provide complementary microscopic information on proton diffusion as they capture the dynamic distortions of the lattice caused by thermal motion. A careful analysis of the proton jumps between different environments confirmed that the inwards and outwards bending states are relevant for the understanding of proton diffusion. Indeed, intra-octahedral jumps were shown to only occur starting from an outwards configuration while the inwards configuration seems to favor rotations around the oxygen. On average, in the DFT-MD simulations, the hydrogen bond lengths are shorter for the outwards configuration which facilitates the intra-octahedral jumps. Diffusion coefficients and activation energies were also determined and compared to previous theoretical and experimental data showing a good agreement with previous data corresponding to local proton motion.C. M. acknowledges an Oppenheimer Research Fellowship from the School of Physical Sciences from the University of Cambridge. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 714581). Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service. MAG’ work was supported by the National Science Foundation under grant DMR 1709975 and the Mount Holyoke College Department of Chemistry. Computational resources were provided in part by the MERCURY consortium under NSF grant CHE 1626238