molecular dynamics skills

xjtulyc/awesome-rosetta-skills

Skill Claude CodeCodex

Atomic Simulation Environment (ASE) for atomistic simulations: structure building, geometry optimization, NEB, molecular dynamics, and trajectory analysis.

chatmaterials/lammps-workflows

Skill Claude CodeCodex

Use when the task involves LAMMPS atomistic simulation workflows, including input script creation, minimize, NVT, NPT, and restart setups, force-field and data-file checks, log.lammps review, restart handling, and scheduler scripts.

krisss0mecom/AlphaDynamics

Skill Claude CodeCodex

Run AlphaDynamics protein torsion-dynamics prediction. Use when user wants to predict, analyze, or compare backbone dihedral (phi/psi) ensembles for a peptide / short protein sequence — e.g. "predict torsions for AAAY", "what conformations does KLVFFAE adopt", "compare AAAY vs AAAW", "Ramachandran for [sequence]". The…

thematteroftime/agentic-md-for-dummies

Skill Claude CodeCodex

Use when a user wants to bootstrap an experiment-orchestration skill for their own simulation framework. Captures their framework profile via 17 questions, then emits a tailored paper-to-experiment skill (templates, schema, registry, validator) into their .claude/skills/.

thematteroftime/agentic-md-for-dummies

Skill Claude CodeCodex

Use when reproducing a physics paper (or part of one) in this MD framework. Walks a paper PDF through the design template + registry, validates against the schema, registers any new force/analyzer/visualizer in the framework's forwarding station, and emits a runnable configs/plan.json. Used at the start of any new…

Ling-MD/md-agent-skills

Skill Claude CodeCodex

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…

Ling-MD/md-agent-skills

Skill Claude CodeCodex

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…

Ling-MD/md-agent-skills

Skill Claude CodeCodex

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…