Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native…
安装
npx skills add K-Dense-AI/drug-discovery-agent-skills --skill molecular-dynamicsnpx skills add K-Dense-AI/drug-discovery-agent-skills --skill molecular-dynamics -a claude-code -gnpx skills add K-Dense-AI/drug-discovery-agent-skills --skill molecular-dynamics -a codex -ggemini skills install https://github.com/K-Dense-AI/drug-discovery-agent-skills.git --path skills/molecular-dynamicsgh skill install K-Dense-AI/drug-discovery-agent-skills molecular-dynamicsgit clone --depth 1 https://github.com/K-Dense-AI/drug-discovery-agent-skills /tmp/K-Dense-AI__drug-discovery-agent-skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/K-Dense-AI__drug-discovery-agent-skills/skills/molecular-dynamics ~/.claude/skills/molecular-dynamics # Claude Code
cp -R /tmp/K-Dense-AI__drug-discovery-agent-skills/skills/molecular-dynamics ~/.agents/skills/molecular-dynamics # Codex, Cursor, Gemini CLI, Copilot, OpenCode