Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
Install
npx skills add K-Dense-AI/scientific-agent-skills --skill molecular-dynamicsnpx skills add K-Dense-AI/scientific-agent-skills --skill molecular-dynamics -a claude-code -gnpx skills add K-Dense-AI/scientific-agent-skills --skill molecular-dynamics -a codex -ggemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path skills/molecular-dynamicsgh skill install K-Dense-AI/scientific-agent-skills molecular-dynamicsgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills /tmp/K-Dense-AI__scientific-agent-skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/molecular-dynamics ~/.claude/skills/molecular-dynamics # Claude Code
cp -R /tmp/K-Dense-AI__scientific-agent-skills/skills/molecular-dynamics ~/.agents/skills/molecular-dynamics # Codex, Cursor, Gemini CLI, Copilot, OpenCode