Complete Molecular Dynamics Simulation Archive Generated with a Deterministic End-to-End Workflow for 91 Mineral–Water Systems

This dataset contains the complete molecular dynamics simulation archive generated during the operational validation of a deterministic end-to-end workflow for constructing mineral–water interfacial systems. The archive is provided as a single ZIP file containing 91 completed simulation directories. The systems cover hematite, magnetite, and goethite; multiple crystallographic facets; arsenic- and fluoride-containing aqueous environments; acidic, neutral, and basic chemical conditions; and background salinity levels corresponding to 0, 5, 10, 20, 30, and 50 NaCl ion pairs. Each directory contains the files generated and used during the corresponding workflow execution, including system configurations, crystallographic and molecular inputs, force-field parameters, PACKMOL and LAMMPS input files, processed structures, minimized and heated systems, production trajectories, LAMMPS logs, workflow execution records, and the Python scripts employed for system construction, conversion, sanitization, simulation execution, and analysis. This dataset supports the manuscript entitled “A Deterministic End-to-End Workflow for Automated Construction and Validation of Mineral–Water Molecular Dynamics Systems.” The dataset is intended to support verification, reproducibility, reuse of the generated molecular dynamics systems, and further methodological development in automated atomistic simulation of solid–liquid interfaces.