This dataset contains GROMACS molecular dynamics simulation input files for the calcium-free Atlantic cod allergen Gad m 1 (PDB ID: 2MBX) under eight combinations of thermal and pressure processing conditions (300 K, 325 K, 350 K, and 375 K at 1 bar and 3 kbar), performed in triplicate over a 200 ns timescale. Files include topology, coordinate, parameter (.mdp), position restraint, force field, and job submission scripts used for simulations on the Narval supercomputer (Digital Research Alliance of Canada). This dataset supports Part I of a two-part study on the structural dynamics of Gad m 1 under thermal and pressure processing.