用于Harpagide与MMP9结合分子动力学模拟的输入文件

README for Molecular Dynamics Simulation Input Files ===================================================== Software: GROMACS 2020.6_GPU Force field: Amber99SB-ILDN Water model: TIP3P Temperature: 310 K Pressure: 1 bar Simulation time: 100 ns File descriptions: - topol.top: Main topology file for Harpagide-MMP9 complex - result_solv.gro: Solvated initial coordinate file - *.mdp: Parameter files for energy minimization (em), NVT, NPT, and production MD (100 ns) - *.ndx: Index files for analysis - *.itp: Position restraint and topology include files - *.pdb: Structure files for visualization - gmx_mmpbsa.bsh: MM/PBSA binding free energy calculation script - MD_commands.txt: Complete GROMACS command script for all simulation steps Missing files: None. These input files are sufficient to reproduce all simulation results. Raw trajectory files (>30 GB) are not included due to their large size but can be fully reproduced using these input files and the provided GROMACS commands. Contact: corresponding author of the associated manuscript Date: 2026-04-08