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molecular-dynamics

80 / 100 · Low risk

Fine to try.

By ssinder/bioinformatics-agent-skills (GitHub) · research · 75 stars · scanned at commit 42cf1a9

Analyses molecular-dynamics trajectories with a self-contained pure-numpy DCD and PDB trajectory parser plus built-in Kabsch-Sander alignment, SVD-based PCA, hierarchical clustering of RMSD matrices, geometric hydrogen-bond detection, RMSF, radius of gyration, Ramachandran analysis, inter-chain contacts and Shrake-Rupley SASA. This skill should be used when trajectory RMSD or RMSF, PCA, conformational clustering, hydrogen-bond occupancy, Ramachandran plots or solvent-accessible surface analysis…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'molecular-dynamics' ] || [ -L ~/.agents/skills/'molecular-dynamics' ]; then echo 'A skill folder named molecular-dynamics already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/ssinder/bioinformatics-agent-skills' "$d" && git -C "$d" checkout --quiet '42cf1a9c2381b25047dae98ca944ee7b52781ed8' -- 'skills/molecular-dynamics' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/molecular-dynamics' ~/.agents/skills/'molecular-dynamics' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'molecular-dynamics' ~/.claude/skills/'molecular-dynamics' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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