Agent skill · research science · k-dense-ai
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.
Why this skill is useful
Adds executable scripts for preparing systems and performing energy minimization in molecular dynamics simulations that are not commonly found in public documentation.
What it needs
Requires mdanalysis, nglview, openmm installed locally. About 6k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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: 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 simulations: Model proteins in lipid bilayers Intrinsically disordered proteins: Study IDR conformational ensembles 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. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/molecular-dynamics