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
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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