Molecular Dynamics

What it does

Guides Claude through a full MD pipeline with ready-to-run Python code:

• System prep: load PDB, repair with PDBFixer, add hydrogens, solvate with a 10 Å water box at 150 mM NaCl
• Force fields: selection table for AMBER14, CHARMM36m, ff19SB, plus OpenFF/GAFF2 ligand parameterization
• Simulation: energy minimization → NVT equilibration → NPT equilibration/production, automatic CUDA/OpenCL/CPU platform fallback, checkpoint reporters
• Analysis: MDAnalysis RMSD, per-residue RMSF, protein–ligand contact tracking, matplotlib plots
• Best practices: 2 fs timestep with HBonds constraints, PME electrostatics, discarding the equilibration portion

Who it's for

• Structural biologists, computational chemists, and graduate students
• Drug discovery teams validating ligand binding modes and residence time
• Researchers quantifying how mutations change protein flexibility
• Anyone preferring a Python workflow over GROMACS/NAMD scripting

Examples

1. "Build a script that solvates 1UBQ and runs 1 ns of NPT production MD" → full pipeline from PDBFixer cleanup to production reporters
2. "Plot backbone RMSD and per-residue RMSF from npt_traj.dcd" → aligned trajectory analysis with saved PNG figures
3. "Parameterize this SMILES ligand with OpenFF and list contact residues within 4.5 Å per frame" → ligand parameterization plus contact-map analysis code

Install the skill I found on Claude Skill Mart.
Copy the skills/molecular-dynamics folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/molecular-dynamics/.
When it's done, tell me in one line what this skill can do.