Molecular Dynamics

If you need to run molecular dynamics simulations without leaving Claude, this wraps OpenMM and MDAnalysis into a usable workflow. You get system prep from PDB files, energy minimization, NVT/NPT equilibration with proper barostat setup, and trajectory analysis like RMSD and RMSF calculations. The code examples show real GPU-accelerated simulation setup with force fields like Amber14, which is helpful if you're doing protein stability studies or ligand binding work. It's opinionated about things like using PME for electrostatics and HBonds constraints, but that's reasonable for most biomolecular systems. Honestly most useful if you're prototyping simulation parameters or need quick analysis snippets rather than running week-long production runs.

skills.sh installs: 2K
GitHub stars: 56.6K
last updated: Aug 21, 2026

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Install

$ npx -y skills add k-dense-ai/scientific-agent-skills --skill molecular-dynamics --agent claude-code

Installs into .claude/skills of the current project.

Files

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

Reviewed versions: OpenMM 8.6.1 and MDAnalysis 2.10.0. Reference-platform smoke checks use small synthetic systems; GPU performance and scientific convergence are not established by them. OpenMM latest API pages identify a development build, so the installed 8.6.1 API is the executable reference.

Installation into a dedicated environment:

uv venv --python 3.12 .venv-md
uv pip install --python .venv-md/bin/python "openmm==8.6.1" "MDAnalysis==2.10.0" matplotlib pandas
# Windows: use .venv-md/Scripts/python.exe instead