molecular-dynamics

Runs and analyzes molecular dynamics simulations using OpenMM and MDAnalysis. Covers system preparation with PDBFixer and OpenFF/GAFF2, force field choice (AMBER14, CHARMM36m, ff19SB), energy minimization, NVT/NPT equilibration, production MD, and trajectory analysis (RMSD, RMSF, protein-ligand contacts). Use when simulating a protein or protein-ligand system on GPU, assessing how a mutation affects protein dynamics, characterizing ligand binding mode, quantifying per-residue flexibility, or modeling membrane proteins and disordered proteins. Not for GROMACS or NAMD workflows, which the skill lists only as alternatives.

Version

1.1

License

MIT