Directory / Scientific Agent Skills (K-Dense) / molecular-dynamics

molecular-dynamics

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
Description from the SKILL.md front matter.

Install

GitHub CLI v2.90+ (Copilot by default)

gh skill install K-Dense-AI/scientific-agent-skills molecular-dynamics

For Claude Code

gh skill install K-Dense-AI/scientific-agent-skills molecular-dynamics --agent claude-code

For Codex

gh skill install K-Dense-AI/scientific-agent-skills molecular-dynamics --agent codex

Commands follow each host's documentation (Any Agent Skills host (Claude Code, Codex, Cursor, Gemini CLI, Copilot…) docs). gh skill needs GitHub CLI 2.90 or later and is in public preview.

Listed from K-Dense Inc.'s catalog, not reviewed by us. Read the source before installing.

Catalog: Scientific Agent Skills (K-Dense)
Author: Kuan-lin Huang
Source code: K-Dense-AI/scientific-agent-skills
License: MIT
Repository stars: 52,795 for K-Dense-AI/scientific-agent-skills (the whole catalog repo)
Version: 1.3
Added to catalog: Not tracked for this source
Last change: 2026-10-19 (last push to the repo)

What it contains

Skills: 1

Similar in Science, research & learning

13c-metabolic-flux (K-Dense science skill)
adaptyv (K-Dense science skill)
aeon (K-Dense science skill)
alphagenome (K-Dense science skill)
analytical-method-validation (K-Dense science skill)
anndata (K-Dense science skill)