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Molecular Dynamics Simulation

Sets up, runs and analyzes molecular dynamics simulations of proteins and molecules with OpenMM and MDAnalysis.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
3 files

What it does

Molecular dynamics (MD) simulates how atoms in a protein or small molecule move over time using physics equations. With this skill installed, the agent can guide you through preparing a molecular structure, adding water and ions, running energy minimization and equilibration, running production simulations with OpenMM, and analyzing the resulting trajectories with MDAnalysis (for example RMSD, RMSF, contact maps and free energy surfaces). The included notes stress that the setup needs careful system-specific checks and that a simulation alone does not establish binding free energy or residence time.

Great for

  • Structural biologists and biophysicists setting up protein stability or flexibility studies
  • Computational chemists analyzing ligand binding behaviour from trajectories
  • Python developers building MD pipelines who want a tested starting point with OpenMM and MDAnalysis

Skip it if

  • Clinical or medical decisions: simulation outputs are exploratory and do not establish real-world binding or efficacy, so they must not be used to guide treatment.
  • Users without a Python 3.11+ environment or the ability to install OpenMM and MDAnalysis, since the code will not run without them.
  • Long or large production runs on a laptop without GPU support, which can take impractically long; the skill does not establish GPU performance.

Try asking

  • “Prepare a cleaned PDB file of my protein in a water box with 0.15 M salt using the AMBER14 force field.”
  • “Run energy minimization and NVT equilibration on my prepared system, saving outputs with a new prefix.”
  • “Compute RMSD and RMSF from my MD trajectory and plot them with matplotlib.”
  • “Build a contact map and a free energy surface from my simulation trajectory.”
Step-by-step guide: how to use Molecular Dynamics SimulationInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 3 original files, the MIT licence and an attribution note.

    molecular-dynamics.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip molecular-dynamics.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip molecular-dynamics.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Use a dedicated virtual environment as the SKILL.md instructs, and pin the reviewed OpenMM and MDAnalysis versions.
  • Inspect your input structure first (missing loops, protonation, ligands, alternate locations) before trusting any simulation result.
  • Use a fresh output prefix for each stage so earlier results are not overwritten, and test on the CPU platform before relying on a GPU.

What's inside

  • references/mdanalysis_analysis.md
  • references/system_preparation.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.