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#diffusion models Dataset Open access

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

Jerry Peprah Owusu
Aug 2026 · Zenodo (CERN European Organization for Nuclear Research)

Abstract

This dataset contains all input files, simulation results, and a master data table from molecular dynamics (MD) simulations of ion transport in electrolyte-filled slit nanopores, performed with GROMACS version 2024.2. Both charge-neutral and surface-charged pore systems are included. The associated publication is: "Interfacial adsorption and field-assisted hopping govern ion conductivity in electrolyte-filled nanopores" Simulation Input Files 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 ffnonbonded.itp, which can be varied 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 defined in ffnonbonded.itp and in the topology files CG_bot_charged.itp and CG_top_charged.itp, which specify the charge distribution on the bottom and top pore walls, respectively. Initial configuration files and run parameter files (grompp.mdp) are provided for all systems. Master Data Table A CSV file (simulation_master_table.csv) is included in which each row corresponds to a single simulation and columns specify the pore width, ionophilicity parameters, surface charge density, applied electric field, system composition, and all key extracted results (ionic current, Green–Kubo conductivity, ion-pairing correlation factor, diffusion coefficients, and adsorption free energies). This file provides a complete mapping between simulation parameters and results. Simulation Results — Neutral Pores Results are provided across five pore widths (H = 0.9, 1.9, 2.6, 4.8, and 9.2 nm) and eight ionophilicity values: Ionic current under applied electric fields of 0.0–1.0 V/nm, with block-averaging standard errors, extracted via the Helfand moment method. Green–Kubo conductivity (σ_GK), Nernst–Einstein conductivity (σ_NE), cross-correlation conductivity (σ_cross), and the ion-pairing correlation factor (β), computed from zero-field equilibrium simulations. In-plane diffusion coefficients for Na⁺ and Cl⁻ from mean-squared displacement analysis at zero electric field. Adsorption free energies (ΔG_min) for Na⁺ and Cl⁻ from Boltzmann inversion of the equilibrium density profiles. Simulation Results — Charged Pores Results are provided for three pore widths (H = 1.9, 4.8, and 9.2 nm), four surface charge densities (Σ_s = 0.5, 1.0, 1.5, and 2.0 e/nm²), and two ionophilicity values: Total, interfacial, and pore-center ionic currents under applied electric fields of 0.0–1.0 V/nm, with block-averaging standard errors. Simulation Protocols All simulations used the Nosé–Hoover thermostat at 300 K with a relaxation constant of 1.0 ps and the SPC/E water model. Electrolyte concentration was 1 M NaCl. For full details of the simulation protocols, theoretical framework, and analysis methods, please refer to the associated publication. If further clarification is needed, please contact the corresponding author: Mohammad Javad Abdolhosseini Qomi — mjaq@uci.edu

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