packmol-generate-mixture SKILL.md skillA
packmol-generate-mixture from jinzhezenggroup/computational-chemistry-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jinzhezenggroup/computational-chemistry-agent-skills/packmol-generate-mixture@v1.0Pins v1.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jinzhezenggroup/computational-chemistry-agent-skills
- Path
data-processing/packmol-generate-mixture/SKILL.md- Versions recorded
- 3
- Latest version
- v1.0, committed Mar 23, 2026
- First version recorded
- Mar 17, 2026
- Size
- 5,460 bytes
- Repository stars
- 156
- License
- LGPL-3.0
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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# packmol-generate-mixture
Use Packmol to generate an initial **packed** configuration for a molecular mixture.
## Agent responsibilities (do these in order)
1. **Collect inputs** (ask if missing; do not guess):
- component structure files (XYZ), one per species (e.g. `species1.xyz`, `species2.xyz`)
- molecule counts for each species (e.g. `species1: 100`, `species2: 650`)
- **either** target density (g/cm^3) **or** a fixed cubic box length (Å)
- Packmol `tolerance` (Å)
- **output location**: output directory + output filename prefix (system name)
1. **Validate inputs**:
- confirm XYZ files exist and are readable
- confirm the first line (atom count) matches the number of coordinate lines
- if density-based box estimation is requested: confirm each molecule’s elemental composition can be inferred from the XYZ symbols
1. **Decide box size**:
- If user provides `box_length_A`: use it.
- Else compute `box_length_A` from density (see formula below).
1. **Create a working folder** at the requested output location:
- copy the component XYZ files into it (or reference them with absolute paths)
1. **Write Packmol input** `${system_name}.inp`:
…Read the whole file at its exact version.
How to install
mdr add jinzhezenggroup/computational-chemistry-agent-skills/packmol-generate-mixture@sha256:3714760d9d26d1b0The line at the top of this page pins the label v1.0, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_xbaw2dzolwbp3u7x)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Mar 17, 2026 and Mar 23, 2026, about one every 3 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.0 latest | 2026-03-23 | 622da72 | 5,460 B | A | view · diff |
| v1.0 | 2026-03-21 | 0fbe96d | 5,433 B | A | view · diff |
| v1.0 | 2026-03-17 | d0e4cd7 | 5,383 B | A | view |
Audit of the latest version
- 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
jinzhezenggroup/computational-chemistry-agent-skills · 156 stars · license LGPL-3.0 · pushed 2026-11-02 · 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
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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