# Archive of YiiP membrane-protein system trajectories Data for the publication * Adel Hussein, Shujie Fan, Maria Lopez-Redondo, Ian Kenney, Xihui Zhang, Oliver Beckstein, and David L. Stokes. Energy coupling and stoichiometry of Zn²⁺/H⁺ antiport by the cation diffusion facilitator YiiP. eLife, Apr 2023. doi: https://doi.org/10.7554/elife.87167.1 *Equilibrium simulations* were performed with [GROMACS](https://www.gromacs.org) 2021.1. *CpHMD* simulations were performed using [CHARMM](https://www.charmm.org) c42a2 with PHMD. The original simulation trajectories were originally saved at 10 ps time intervals but in order to decrease the size we rewrote them at 1 ns intervals for equilibrium simulations and 100 ps intervals for CpHMD simulations. The trajectories are otherwise like the raw GROMACS trajectories: all atoms are included and no PBC corrections were performed. The CpHMD simulations were originally DCD files, and they were converted into GROMACS XTC files to reduce the size. The TPR files are the GROMACS run input files that were used to run the simulations. The initial coordinates of the system were the same for all three repeat runs and only the random seed was changed, thus resulting in diverging trajectories. The initial coordinates are supplied as `md.gro`. CpHMD simulations were performed as pH-replica exchange. All raw output files necessary to obtain the deprotonated fraction as function of pH as shown in the paper are included. See the linked GitHub repository for code (which makes use of code from https://github.com/Hendejac/CpHMD-Analysis). # Directories - **apo** - topology: GROMACS topology files (produced by CHARMM-GUI) - traj: YiiP was prepared without Zn2+ ions in the binding sites. 3 x 1000 ns (independent repeats `md[0-2].xtc` all starting from same initial coordinates, `md.gro`) - **holo** - topology: GROMACS topology files (produced by CHARMM-GUI) - traj: YiiP was prepared with Zn2+ ions in all the 3 binding sites. 3 x 1000 ns (independent repeats `md[0-2].xtc` all starting from same initial coordinates, `md.gro`) - **empty_site_B** - topology: GROMACS topology files (produced by CHARMM-GUI) - traj: YiiP was prepared with Zn2+ ions in site A and site C, leaving site B empty. 6 x 1000ns (independent repeats `md[0-5].xtc` all starting from same initial coordinates, `md.gro`) - **D72A** - topology: GROMACS topology files (produced by CHARMM-GUI) - traj: YiiP was prepared with the D72A mutation and Zn2+ ions in all the 3 binding sites. 3 x 1000ns (independent repeats `md[0-2].xtc` all starting from same initial coordinates, `md.gro`) - **CpHMD** - topology: Initial structure and setting files for the CpHMD simulation with CHARMM. - traj: YiiP was prepared without Zn2+ ions in the binding sites. - production: log files and lamb files that contain the data of replica exchange and titration coordinates.