packmol
Build Packmol Molecular Systems
Preparing molecular dynamics starting structures requires precise Packmol syntax and geometry choices. This skill helps create inputs, solvation setups, interfaces, and validation steps for Packmol workflows.
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Review the Skillstore skill "packmol" from https://skillstore.io/skills/chenghao-wu-packmol.md and its manifest at https://skillstore.io/api/skills/chenghao-wu-packmol/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "packmol". User asks for a 1000-water simulation box.
Expected outcome:
A Packmol setup plan with tolerance, box dimensions, structure count, output name, and validation checks.
Using "packmol". User asks to solvate a charged protein.
Expected outcome:
A protein solvation workflow with shell size, estimated ions, periodic box guidance, and success checks.
Using "packmol". User reports a failed interface packing run.
Expected outcome:
A troubleshooting summary covering constraint conflicts, molecule counts, tolerance, and incremental testing.
Security Audit
SafeMost static findings are false positives from Markdown code fences, relative documentation links, scientific terms, and reference URLs. The helper scripts write explicit output files and optionally run a fixed packmol command without shell interpolation. No prompt injection, data exfiltration intent, or hidden malicious behavior was found.
Risk Factors
📁 Filesystem access (21)
⚙️ External commands (77)
🌐 Network access (5)
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https://skillstore.io/skills/chenghao-wu-packmol/audits/8?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_reportMarkdown badge
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<a href="https://skillstore.io/skills/chenghao-wu-packmol?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/chenghao-wu-packmol/security.svg" alt="Skillstore security assessment" loading="lazy"></a>Embed card
<iframe src="https://skillstore.io/embed/skills/chenghao-wu-packmol.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
Chenghao-Wu. (2026). packmol security audit report (audit version 8) [Author version 1.0.0]. Skillstore. https://skillstore.io/skills/chenghao-wu-packmol/audits/8BibTeX citation
@techreport{chenghao-wu-chenghao-wu-packmol-2026,
author = {Chenghao-Wu},
title = {packmol security audit report (audit version 8)},
institution = {Skillstore},
year = {2026},
number = {8},
url = {https://skillstore.io/skills/chenghao-wu-packmol/audits/8},
note = {Author version 1.0.0}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "packmol security audit report (audit version 8)"
version: "1.0.0"
type: report
authors:
- name: "Chenghao-Wu"
date-released: "2026-07-05"
url: "https://skillstore.io/skills/chenghao-wu-packmol/audits/8"
identifiers:
- type: other
value: "skillstore:chenghao-wu-packmol:audit:8"
description: "Skillstore immutable audit report identifier"
Skillstore Score
Why this score Evidence Confidence: HighWhat You Can Build
Prepare a Solvent Box
Create a clear Packmol plan for single-component or mixed-solvent boxes.
Solvate a Biomolecule
Set up water, ions, box dimensions, and validation checks for a protein system.
Build Interface Systems
Design liquid-liquid or liquid-vapor interfaces with plane constraints and density checks.
Try These Prompts
Create a Packmol input for 500 water molecules in a 30 angstrom cubic box. Include validation steps.
Build a Packmol plan for an 80:20 water ethanol mixture in a 40 angstrom box.
Help solvate protein.pdb with a 15 angstrom shell, neutralizing ions, and 0.15 M salt.
Review my Packmol constraints and explain why packing may not converge. Suggest safe parameter changes.
Best Practices
- Start with small molecule counts before scaling to large production systems.
- Set a reproducible seed when comparing packing outcomes.
- Validate output geometry with overlap and density checks before MD setup.
Avoid
- Do not assume Packmol output is physically equilibrated.
- Do not use incompatible molecule files without checking atom names and formats.
- Do not increase molecule counts before resolving constraint conflicts.
Frequently Asked Questions
What does this skill help create?
Can it run Packmol for me?
Does it generate force-field files?
Can it help with failed convergence?
Which file formats are covered?
Is scientific validation still required?
Developer Details
Author
Chenghao-WuLicense
MIT
Author version
v1.0.0
Skillstore revision
r1
Ref
02f077c174c5335e2f5d02ca15e77b70d9543e58
Maintenance freshness
7/18/2026
Usage
10 downloads · 281 views