Coarse-Grained Molecular Dynamics Simulation Dataset for Peptide-Lipid Interaction

This dataset contains the coarse-grained molecular dynamics simulations used to analyze peptide-lipid interactions using the Martini 3 force field. The system was constructed and coarse-grained following standard Martini workflows, and simulations were performed with GROMACS 2023. After energy minimization with a steepest-descent algorithm, the system underwent several equilibration stages designed to stabilize temperature, pressure, and membrane mechanics. Early equilibration used a gentle thermostat-barostat combination to relax the system, followed by a final equilibration phase employing more accurate coupling schemes suitable for production. The production simulation was run with a 20-fs timestep under semi-isotropic pressure coupling and a temperature-controlled ensemble appropriate for Martini CG simulations. The dataset includes all files required to reproduce the simulation workflow: the mdp parameter file, full topologies (top + itps), the compiled tpr with the complete setup, the initial configuration, the final configuration, and the full trajectory.