jinzhezenggroup/computational-chemistry-agent-skills · data-processing/packmol-generate-mixture/SKILL.md

packmol-generate-mixture skillA

packmol-generate-mixture is agent-read markdown (skill) from jinzhezenggroup/computational-chemistry-agent-skills: A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. USE WHEN you need to randomly pack a specific number of molecules into a simulation box (defined by target density or fixed lengths) to create starting geometries for molecular dynamics or related computational chemistry workflows..

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 jinzhezenggroup/computational-chemistry-agent-skills/packmol-generate-mixture@v1.0
Exact content
mdr add jinzhezenggroup/computational-chemistry-agent-skills/packmol-generate-mixture@sha256:3714760d9d26d1b0

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_xbaw2dzolwbp3u7x.svg)](https://markdownregistry.com/a/art_xbaw2dzolwbp3u7x)

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Versions

versioncommittedcommitsizeaudit
v1.0 latest2026-03-23 622da72 5,460 BA view · diff
v1.02026-03-21 0fbe96d 5,433 BA view · diff
v1.02026-03-17 d0e4cd7 5,383 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 (5460 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

jinzhezenggroup/computational-chemistry-agent-skills · 138 stars · license LGPL-3.0 · pushed 2026-09-18 · branch master

API

GET https://markdownregistry.com/api/v1/artifacts/art_xbaw2dzolwbp3u7x
GET https://markdownregistry.com/api/v1/resolve?ref=jinzhezenggroup/computational-chemistry-agent-skills/packmol-generate-mixture
GET https://markdownregistry.com/api/v1/blob/3714760d9d26d1b0f78fd5674b08de766c9a312e44439aaf5b22d3127542b48f

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