Data for: Emergent Mechanisms of Proton-Coupled Transport from Molecular Simulations

Compressed files containing primary data for the following publication: "Emergent Mechanisms of Proton-Coupled Transport from Molecular Simulations" J. D. Colburn, N. A. Mouroug, P. C. Biggin Proceedings of the National Academy of Sciences (2026) proton_transfer_qmmm.zip QM/MM metadynamics simulations of proton transfer between D205 and D305 in cystinosin in various states. For each state: trajectories of the protein and QM region, the full starting snapshot, deposited hills, final free-energy profile, as well as run inputs. conformational_us.zip Umbrella sampling MD simulations of cystinosin alternating access. For each system: the collective-variable time series with WHAM settings and the published PMF, starting structures for every window, the PLUMED input with the PCA reference, and full-system trajectories of the most outward- and inward-facing windows. Additional detail is provided in README.md.