Codex/Cursor Agent Skills for GROMACS MD workflows and publication-ready PyMOL figures
Skill Codex
Use when working on classical biomolecular molecular dynamics with GROMACS: system setup, pdb2gmx/topology preparation, ligand parameterization, solvation and ions, energy minimization, NVT/NPT equilibration, production MD, trajectory analysis, MM/PBSA-style post-processing, .mdp parameter review, GROMACS command…
Skill Codex
Use when creating, improving, or troubleshooting publication-ready molecular structure figures with PyMOL: protein cartoons, ligand binding pockets, surfaces, electrostatic-style views, hydrogen bonds, labels, structure alignments, MD representative snapshots, transparent PNG export, ray tracing, journal-quality…
Skill Codex
Use when creating reusable PyMOL figures for protein-protein or chain-chain interfaces from PDB/MD snapshot files, especially when the user wants only protein kept, water/ions/ligands removed, inter-chain hydrogen-bonding residues shown as sticks, green dashed hydrogen bonds, chain-colored cartoons and labels…