Molecular Dynamics Input Files for Harpagide-MMP9 Binding Simulation

Fen Lou provides GROMACS input files for a 100-nanosecond molecular dynamics simulation of the Harpagide ligand binding to the MMP9 protein. The 170.2 MB collection includes topology, parameter, coordinate, and analysis script files sufficient to reproduce the full simulation. The dataset was published on the figshare platform in April 2026.

Use Cases

• Reproduce a 100 ns MD simulation of Harpagide-MMP9 binding using the provided `topol.top`, `result_solv.gro`, and `*.mdp` parameter files.
• Calculate MM/PBSA binding free energy for the complex using the included `gmx_mmpbsa.bsh` script and associated topology files.
• Analyze simulation trajectories by generating index groups with the provided `*.ndx` files for specific protein or ligand atoms.
• Visualize the initial and simulated structures using the included `*.pdb` and coordinate files for molecular rendering.
• Execute the complete simulation workflow from energy minimization to production MD using the command sequence in `MD_commands.txt`.

Strengths

• Includes all necessary input files (topology, parameters, coordinates, scripts) to fully reproduce a 100-nanosecond molecular dynamics simulation.
• Simulation parameters are explicitly documented, specifying the GROMACS 2020.6_GPU software, Amber99SB-ILDN force field, TIP3P water model, 310 K temperature, and 1 bar pressure.
• Released under a permissive CC-BY-4.0 license, allowing for reuse and modification with attribution.

Limitations

• The raw trajectory data files, which exceed 30 GB, are not included, requiring users to run the simulation to obtain them.
• The dataset is specific to a single protein-ligand pair (MMP9 and Harpagide), limiting generalizability to other systems without modification.
• Sample size is one simulation system; no replicates or alternative conformational states are provided.

Provenance

Source

Fen Lou, likely associated with an academic manuscript.

Collection Method

Created as input files for a molecular dynamics simulation using GROMACS software.

Time Range

Simulation time is 100 nanoseconds.

Freshness

Dataset reflects state from a simulation conducted circa 2026.

Geography

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