k-dense-ai/scientific-agent-skills · skills/molecular-dynamics/SKILL.md

molecular-dynamics skillA

molecular-dynamics is agent-read markdown (skill) from k-dense-ai/scientific-agent-skills: 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..

Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.

How to install

Latest version
mdr add k-dense-ai/scientific-agent-skills/molecular-dynamics@v1.1
Exact content
mdr add k-dense-ai/scientific-agent-skills/molecular-dynamics@sha256:ca248ad20180a5ae

Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.

Badge

mdr badge

[![mdr](https://markdownregistry.com/badge/art_vb2uxl3iavsxoqsg.svg)](https://markdownregistry.com/a/art_vb2uxl3iavsxoqsg)

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Versions

versioncommittedcommitsizeaudit
v1.1 latest2026-07-31 4226ca8 14,721 BA view · diff
v1.02026-07-31 bd99c01 14,721 BA view · diff
v1.02026-07-26 b085e11 14,715 BA view · diff
git:20260611.1b8fae32026-06-11 1b8fae3 14,720 BA view

Audit of the latest version

A  17 of 17 checks passed. Deterministic, no model, same answer every run.
  • pass: Frontmatter block present
  • pass: Frontmatter declares a name
  • pass: Frontmatter declares a description
  • pass: Size between 200 bytes and 200 KB (14721 bytes)
  • pass: No zero-width or bidi control characters
  • pass: No instruction hidden inside an HTML comment
  • pass: No link to an exfiltration or paste host
  • pass: No credential-shaped string
  • pass: No instruction to send local credentials anywhere
  • pass: No text hidden with inline styles
  • pass: No prompt-injection phrasing
  • pass: No curl or wget piped into a shell
  • pass: No recursive delete of root, home or parent
  • pass: No instruction to read or print local credentials
  • pass: No base64 blob over 200 characters
  • pass: No link to a raw IP address
  • pass: No script tag

Source

GitHub

k-dense-ai/scientific-agent-skills · 45,352 stars · license MIT · pushed 2026-09-14 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_vb2uxl3iavsxoqsg
GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/molecular-dynamics
GET https://markdownregistry.com/api/v1/blob/ca248ad20180a5ae1dc053a9b9eb13ba3a04f467783ed073b1fa4f37d59a580b

Agents talk at modelranch.com: hand yours the instructions there and it joins the network that reads files like this one.