Molecular Dynamics Simulations of Ion Transport in Ionophilic Nanopores — Neutral and Charged Systems

This dataset contains all input files and simulation results from molecular dynamics (MD) simulations of Na⁺ and Cl⁻ ion transport through 5 nm-wide ionophilic slit nanopores, performed with GROMACS version 2024.2. Both neutral and surface-charged pore systems are included. Simulation Input Files All GROMACS input files necessary to reproduce the simulations are provided for both neutral and charged pore systems. The surface–ion interaction strength (ionophilicity) is controlled through the Lennard-Jones parameters in the ffnonbonded.itp force field file, allowing systematic variation of the surface epsilon parameter across eight values for the neutral case and two representative values (low and high ionophilicity) for the charged case. For the charged systems, the surface charge density is set both in ffnonbonded.itp and in the topology files CG_bot_charged.itp and CG_top_charged.itp, which define the charge distribution on the bottom and top simplified pore walls, respectively. Initial configuration files are also provided for all systems. Simulation Data The dataset includes two types of output data: Diffusion coefficients — Parallel (axial) diffusion coefficients for Na⁺ and Cl⁻ computed at zero electric field via mean squared displacement analysis. For the neutral system, these are provided across five pore widths (1, 2, 3, 5, and 10 nm) and eight ionophilicity values. For the charged system, values are reported for pore widths of 5 and 10 nm, four surface charge densities (0.50, 1.00, 1.50, and 2.00 e/nm²), and two ionophilicity values. Drift velocities — Ion drift velocities for Na⁺ and Cl⁻ under applied electric fields ranging from 0.0 to 1.0 V/nm (neutral system) or 0.0 to 1.0 V/nm in steps of 0.2 V/nm (charged system), reported alongside statistical uncertainties. These are provided as a function of pore size, surface charge density, and ionophilicity parameter. For details regarding simulation protocols, experimental conditions, and system setup, please refer to the associated publication. If further clarification is needed, please contact the corresponding author:Mohammad Javad Abdolhosseini Qomi – [e-mail]