These data sets contain files associated with all-atom molecular dynamics simulations of the neurotransmitter release machinery between two flat bilayers or between a flat bilayer and a vesicle. Each directory corresponds to one simulation as described in the reference associated with this deposition and summarized in Table 1 of that reference. The simulations were performed with gromacs. For each simulation, filenames have a common beginning (e.g. prsg for the simulation in the prsg directory) followed by a few letters that indicate the nature or order of the simulation: nvt for temperature equilibration runs; par for pressure equilibration runs and mdx for production simulations, where x is a number that denotes the order of a particular run within the chain of concatenated simulations. The filename extensions follow the common gromacs nomenclature. Here is a list of the types of files included in the deposition. Filenamea.sh or Filenameb.sh: text files with the SLURM instructions to run the simulation. These files show which files were used to run the particular simulation. Filename.top: topology file that includes calls to the force field and to other topology files and/or restraint files Filename.itp: topology or restraint file Filename.ndx: index file Filename.mdp: file containing the molecular dynamics parameters Filename.log: log file for the simulation Filename.gro: file with the coordinates and velocities at the end of the simulation Filename.cpt: checkpoint file containing the final coordinates and velocities with high precision to continue the simulation Filaname.edr: energy file Filenamecenterfit.pdb: selected frames that have been aligned with the initial configuration and converted to PDB format. In addition, each simulation directory contains force field, restraint and/or topology directories. The filename.xtc trajectory files that contain coordinates and velocities of frames saved during the simulations are not included because of their large size, which would render the deposition very expensive. These files are available from Josep Rizo upon reasonable request. This is the contact information: Name: Josep Rizo Institution: Department of Biophysics, UT Southwestern Medical Center Dallas Address: 6001 Forest Park Road, Dallas, TX 75390-8816 Email: Jose.Rizo-Rey@UTSouhtwestern.edu