Cantera Ignition Delay
K-Dense-AI/scientific-agent-skills
Runs Cantera constant-volume or constant-pressure ignition simulations and reports temperature-based ignition delay with mechanism provenance and checks.
This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular dynamics", or…
Install Packmol
$ npx skills add aiskillstore/marketplace --skill packmol -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aiskillstore/marketplace packmol --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chenghao-wu/packmol .claude/skills/packmol && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "packmol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/chenghao-wu/packmol into .claude/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/aiskillstore/marketplace/tree/main/skills/chenghao-wu/packmolType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add aiskillstore/marketplace --skill packmol -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aiskillstore/marketplace packmol --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/chenghao-wu/packmol .agents/skills/packmol && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "packmol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/chenghao-wu/packmol into .agents/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aiskillstore/marketplace --skill packmol -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aiskillstore/marketplace packmol --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/chenghao-wu/packmol .cursor/skills/packmol && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "packmol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/chenghao-wu/packmol into .cursor/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/aiskillstore/marketplace.git --path skills/chenghao-wu/packmol--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add aiskillstore/marketplace --skill packmol -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aiskillstore/marketplace packmol --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/chenghao-wu/packmol .gemini/skills/packmol && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "packmol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/chenghao-wu/packmol into .gemini/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install aiskillstore/marketplace packmolInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add aiskillstore/marketplace --skill packmol -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/chenghao-wu/packmol .github/skills/packmol && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "packmol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/chenghao-wu/packmol into .github/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aiskillstore/marketplace --skill packmol -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aiskillstore/marketplace packmol --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/chenghao-wu/packmol .opencode/skills/packmol && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "packmol" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/chenghao-wu/packmol into .opencode/skills/packmol/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "packmol", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
packmol- GitHub stars
- 430
- Token cost
- ~2.9k tokens
- SKILL.md length
- 833 words
- Files
- 24 (incl. scripts, references)
- Skills in repo
- 1,108
- Repo updated
- First seen
- Licence
- None found
At a glance
This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular dynamics", or…
- Works in 4 steps: Basic Molecular Packing → Protein Solvation → Interface Systems → …
- Asks to create a packmol input
- SKILL.md covers What is Packmol?, Installation, Quick Start and Core Concepts, plus 5 more sections
- Runs Python scripts from its folder; calls python and pip
What it does
Packmol is an agent skill from aiskillstore/marketplace. This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular dynamics", or discusses molecular packing, solvation, or building simulation starting structures.
Its SKILL.md is about 2.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 29 other files, including scripts and reference files (for example `examples/basic/README.md`, `examples/interface/README.md` and `examples/solvation/README.md`).
It sits in Research & Science, covering Physical and earth sciences. The repository describes itself as: Security-audited skills for Claude, Codex & Claude Code. One-click install, quality verified.
When your agent uses it
- Asks to create a packmol input
- Pack molecules with packmol
- Solvate a protein
- Build an initial configuration
Example prompts
- “create a packmol input”
- “pack molecules with packmol”
- “solvate a protein”
- “/packmol”
Requirements
- Python 3
Workflow steps
4 steps, taken from the step headings in SKILL.md.
- Basic Molecular Packing
- Protein Solvation
- Interface Systems
- Advanced Constraints
What it can do on your machine
Read from SKILL.md and the folder at commit ad8daf7. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 2 files in scripts/ (Python, from the files we listed), which the agent can run.
Shell commands in SKILL.md call:
pythonpip
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
m3g.github.iogithub.comdoi.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Packmol loads about 2.9k tokens when it runs, and up to ~15k if it reads all its reference files. Until then it costs about 71 tokens; SKILL.md has 833 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 833 words (~2,866 tokens).
“Build initial configurations for molecular dynamics simulations using Packmol.”
- name
- packmol
- version
- 1.0.0
Files
SKILL.md and 23 other files (scripts, references) in skills/chenghao-wu/packmol of aiskillstore/marketplace.
- SKILL.md
- examples/basic/README.md
- examples/basic/mixture.inp
- examples/basic/simple_box.inp
- examples/interface/README.md
- examples/interface/liquid_liquid.inp
- examples/solvation/README.md
- examples/solvation/protein_solvation.inp
- examples/solvation/water_box.inp
- references/constraints.md
- references/file_formats.md
- references/parameters.md
- references/troubleshooting.md
- scripts/analyze_density.py
- scripts/check_overlaps.py
- … and 9 more
Open the folder on GitHubat commit ad8daf7
Compare with similar skills
Packmol next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Packmol this skillaiskillstore/marketplace | 430 | — | ~2.9k | Automated safety check: Pass | None | |
| Cantera Ignition DelayK-Dense-AI/scientific-agent-skills | 48k | 2 repos | ~2.2k | Automated safety check: Pass | MIT | |
| AstropyzLanqing/codex-claude-academic-skills | 4.6k | 14 repos | ~2.9k | Automated safety check: Pass | BSD-3-Clause | |
| PymatgenzLanqing/codex-claude-academic-skills | 4.6k | 12 repos | ~5k | Automated safety check: Pass | MIT | |
| Weathertrpc-group/trpc-agent-go | 1.8k | 9 repos | ~591 | Automated safety check: Pass | Apache-2.0 | |
| Pymol VisualizationChatMol/ChatMol | 372 | — | ~1.2k | Automated safety check: Pass | MIT |
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Weather
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Get current weather and forecasts via wttr.in or Open-Meteo.
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Generate publication-quality molecular visualization images using PyMOL.
Review
Muuuun/luxas
Write domain-authentic review articles that synthesize rather than stack.
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Related
Categories
Questions about Packmol
What does Packmol do?
This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular dynamics", or…. Packmol is an agent skill from aiskillstore/marketplace. This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular dynamics", or discusses molecular packing, solvation, or building simulation starting structures.
When should I use Packmol?
Packmol fits situations like: asks to create a packmol input; pack molecules with packmol; solvate a protein; build an initial configuration.
How do I install Packmol in Claude Code?
Run `npx skills add aiskillstore/marketplace --skill packmol -a claude-code`. Or copy the skill folder (skills/chenghao-wu/packmol in aiskillstore/marketplace) into .claude/skills/packmol in your project. Claude Code loads it when a task matches its description.
How do I install Packmol in Codex?
Run `npx skills add aiskillstore/marketplace --skill packmol -a codex`. Or copy the skill folder (skills/chenghao-wu/packmol in aiskillstore/marketplace) into .agents/skills/packmol in your project. Codex loads it when a task matches its description.
Can I use Packmol in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aiskillstore/marketplace --skill packmol -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/packmol, .gemini/skills/packmol, .github/skills/packmol and .opencode/skills/packmol in your project.
What does Packmol need to run?
Going by SKILL.md and its folder, Packmol needs Python for the scripts in its folder and the command-line tools its instructions call (python and pip). Our summary lists: Python 3.
Does Packmol access the network?
SKILL.md names 3 domains. As links in the text: m3g.github.io, github.com and doi.org. This is read from the text; nothing was executed.
Is Packmol safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Packmol use?
No licence was found for Packmol or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Packmol use?
About 2.9k tokens (SKILL.md is roughly 11k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 12k tokens, read only when the agent opens those files.
What are the alternatives to Packmol?
Skills that share tags, products or a category with Packmol: Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars), Astropy (zLanqing/codex-claude-academic-skills, 4.6k stars), Pymatgen (zLanqing/codex-claude-academic-skills, 4.6k stars) and Weather (trpc-group/trpc-agent-go, 1.8k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Packmol?
aiskillstore (a GitHub organization) maintains it in aiskillstore/marketplace, which has 430 GitHub stars. The repository holds 1,108 skills in this directory. The repository was last updated on October 7, 2026.
Source: aiskillstore/marketplace on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.