Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule systems, assigning force fields, running energy minimization and production MD, and analyzing trajectories (RMSD, RMSF, contact maps, free energy surfaces).
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-molecular-dynamicsnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-molecular-dynamics -a claude-code -gnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-molecular-dynamics -a codex -ggemini skills install https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git --path skills/cheminformatics/alterlab-molecular-dynamicsgh skill install AlterLab-IEU/AlterLab-Academic-Skills alterlab-molecular-dynamicsgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills /tmp/AlterLab-IEU__AlterLab-Academic-Skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/cheminformatics/alterlab-molecular-dynamics ~/.claude/skills/alterlab-molecular-dynamics # Claude Code
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/cheminformatics/alterlab-molecular-dynamics ~/.agents/skills/alterlab-molecular-dynamics # Codex, Cursor, Gemini CLI, Copilot, OpenCode