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Molecular dynamics simulations with OpenMM v1.0.0

Use this resource to prepare, simulate and analyze a molecular dynamics run

New

  • 309 downloads
  • 137 likes
  • 206 saves

Free

Install with the CLI

In a terminal, from the folder you want:

npx --yes palatekit@latest install molecular-dynamics-simulation

With no option, the skill goes to ~/.agents/skills/; add --agent claude-code (or codex, cursor…) to target an agent.

First time: connect the CLI with

npx --yes palatekit@latest login

The agent prepares the system and force field, chains minimization, equilibration and production, then computes trajectory analyses. You get a simulation script and analysis plots.

Mostly picked by

Updated November 2, 2026

Card for the “Molecular dynamics simulations with OpenMM” skill

Details

Works in
Install guides
Generates with
Your agent's model
Licence
MIT

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What you get

  • SKILL.md: full OpenMM workflow, from system to production
  • references/: system preparation and trajectory analysis with MDAnalysis

Good fit for

  • You study protein stability or ligand binding
  • You want the RMSD of an existing trajectory

Not for

    Tags

    • molecular dynamics
    • OpenMM
    • MDAnalysis

    About

    You say

    “Simulate this protein in water, minimize, equilibrate, then compute RMSD over 10 ns.”

    Card for the “Molecular dynamics simulations with OpenMM” skill

    Skill published by k-dense-ai under the MIT license, delivered in its original version.

    Show more

    How to use it

    1. Install the skill in your agent's skills folder
    2. Ask your agent to prepare, simulate and analyze a molecular dynamics run
    3. Review and adjust the result

    Content preview

    Files

    • LICENSE1.1 KB
    • NOTICE-PALATEKIT.md0.5 KB
    • references/mdanalysis_analysis.md9.4 KB
    • references/system_preparation.md4.9 KB
    • SKILL.md19 KB

    Origin and licence

    Listed unmodified

    Author
    k-dense-ai
    Source
    github.com/k-dense-ai/scientific-agent-skills/tree/5f2bc0341354fd5590aef76a533ada1e1e5b4e62/skills/molecular-dynamics
    Licence
    MIT

    Notice

    « molecular-dynamics » (k-dense-ai, MIT) livré dans sa version d'origine : fiche en français et en anglais par PalateKit.

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