Molecular Dynamics
Sets up, runs and analyzes MD simulations with OpenMM and MDAnalysis.
Install
gh skill install K-Dense-AI/scientific-agent-skills molecular-dynamics
Running or analyzing an MD trajectory: system setup, force fields, production runs, RMSD/RMSF, contact maps or binding free energy.
- Author
- Kuan-lin Huang
- License
- MIT
The simulation half covers preparing a system from a PDB file, choosing a force field and water model, solvation, energy minimization, equilibration and GPU production runs through OpenMM. The analysis half uses MDAnalysis on the resulting trajectories: RMSD and RMSF, contact maps, hydrogen bonds and free energy surfaces. It is aimed at questions like how a mutation changes protein flexibility, how long a ligand stays in its binding pose, and what conformations a disordered region actually samples.
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