molecular-dynamics
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.
npx skills add LeonChaoX/qinyan-academic-skills --skill molecular-dynamics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Molecular Dynamics ## Overview Molecular dynamics (MD) simulation computationally models the time evolution of molecular systems by integrating Newton's equations of motion. This skill covers two complementary tools: - **OpenMM** (https://openmm.org/): High-performance MD simulation engine with GPU support, Python API, and flexible force field support - **MDAnalysis** (https://mdanalysis.org/): Python library for reading, writing, and analyzing MD trajectories from all major simulation packages **Installation:** ```bash conda install -c conda-forge openmm mdanalysis nglview # or pip install openmm mdanalysis ``` ## When to Use This Skill Use molecular dynamics when: - **Protein stability analysis**: How does a mutation affect protein dynamics? - **Drug binding simulations**: Characterize binding mode and residence time of a ligand - **Conformational sampling**: Explore protein flexibility and conformational changes - **Protein-protein interaction**: Model interface dynamics and binding energetics - **RMSD/RMSF analysis**: Quantify structural fluctuations from a reference structure - **Free energy estimation**: Compute binding free energy or conformational free energy - **Membrane
- Overview
- When to Use This Skill
- Core Workflow: OpenMM Simulation
- 1. System Preparation
- 2. Energy Minimization
- 3. NVT Equilibration
- 4. NPT Equilibration and Production
- Trajectory Analysis with MDAnalysis
- 1. Load Trajectory
- 2. RMSD Analysis
- 3. RMSF Analysis (Per-Residue Flexibility)
- 4. Protein-Ligand Contacts
- Force Field Selection Guide
- System Preparation Tools
conda install -c conda-forge openmm mdanalysis nglview or pip install openmm mdanalysis
What does the molecular-dynamics skill do?
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.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill molecular-dynamics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.