This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter files are provided for bulk phase simulations as well as for pore simulations with 14 different compounds. The pore simulations are divided into three steps, an energy-minimization, an NVT equilibration, and an NVT production simulation run. For the bulk phase additional constant-pressure simulations are conducted. The provided structure files are for an already equilibrated system. Object files are supplied which can be used to load the generated pores into PoreMS for later alteration and analysis. Results of density and diffusion profiles of pore systems are provided in hdf5 format to be processed with the PoreAna python package.