This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files (directory Mdp) are provided for four simulations - a 2.5 nm pore with one catalyst molecule, a 2.5 nm pore with two catalyst molecules, a 5 nm pore, and a 6 nm pore, all without surface functionalization. The simulation is divided into three steps, an energy-minimization, an NVT equilibration, and an NVT production simulation run. Provided structure files are of an already equilibrated system. Object files are supplied which can be used to load the generated pores into PoreMS for later alteration and analysis. Additionally, short movies can be viewed for the different systems. In the results section, figures from the supporting information are shown.