# Build Packmol Molecular Systems

Preparing valid Packmol inputs is error-prone when systems include solvents, ions, interfaces, or geometric constraints. This skill provides Packmol templates, examples, validation helpers, and troubleshooting guidance for simulation setup.

## Install

```bash
npx skillstore add chenghao-wu/packmol
```

## Metadata

- - Slug: chenghao-wu-packmol
- - Version: 1.0.0
- - Author: Chenghao-Wu
- - GitHub username: Chenghao-Wu
- - License: MIT
- - Repository: https://github.com/Chenghao-Wu/skill\_packmol/tree/main/.claude/skills/packmol
- - Ref: main
- - Supported tools: Claude, Codex, Claude Code
- - Risk level: medium
- - Risk factors: scripts, filesystem, external\_commands
- - Quality score: 50
- - Quality tier: warning
- - Public page: https://skillstore.pages.dev/skills/chenghao-wu-packmol
- - Manifest: https://skillstore.pages.dev/api/skills/chenghao-wu-packmol/manifest

## Capabilities

- Drafts Packmol input files for boxes, mixtures, protein solvation, and liquid interfaces.
- Explains Packmol parameters, constraints, file formats, and common convergence issues.
- Provides Python helpers to generate inputs, validate syntax, inspect overlaps, and analyze density.
- Includes example workflows for basic packing, solvation, and interface systems.
- Guides users on molecule counts, ion placement, solvent shells, tolerances, and restart workflows.

## Use Cases

- Prepare Solvated Protein Inputs: Generate Packmol inputs for a protein with water, ions, box padding, and validation steps before MD preparation.
- Build Mixed Solvent Boxes: Create initial structures for solvent mixtures, additives, and pure liquids using clear molecule counts and box constraints.
- Diagnose Packing Failures: Use troubleshooting references and validation scripts to identify syntax errors, overlaps, density problems, and convergence issues.

## Prompt Templates

### Create a Simple Box

```
Create a Packmol input for 1000 water molecules in a 40 angstrom cubic box. Include the required parameters and explain what files I need.
```

### Set Up Protein Solvation

```
Help me solvate protein.pdb with a 15 angstrom water shell, neutralize a +4 charge, and add 0.15 M salt. Show the Packmol approach and validation steps.
```

### Build a Liquid Interface

```
Design a Packmol input for a water and chloroform interface in a rectangular periodic box. Use plane constraints and include practical molecule-count guidance.
```

### Debug a Failed Packing Run

```
Review my Packmol setup for poor convergence and overlapping atoms. Suggest changes to tolerance, constraints, molecule counts, and validation workflow.
```

## Limitations

- Requires local Packmol and valid molecule structure files to run simulations.
- Does not perform molecular dynamics, force-field assignment, or energy minimization.
- Generated systems still need scientific review before production simulations.
- Helper scripts operate on local files and may overwrite output paths provided by the user.

## Best Practices

- Start with small molecule counts, validate the setup, then scale to the target system size.
- Set a reproducible seed and record tolerance, box size, molecule counts, and structure file versions.
- Always inspect output with overlap, density, and atom-count checks before downstream simulation.

## Anti Patterns

- Do not trust a generated packed structure without scientific validation and visual inspection.
- Do not use very tight boxes or conflicting constraints to force unrealistic density.
- Do not run helper scripts on unreviewed paths when important files could be overwritten.

## Security Audit

- - Safe to publish: true
- - Audited at: 2026-06-28T22:10:26.086\+00:00
- - Summary: The static analyzer reported many high-risk patterns, but review shows most are false positives from markdown code fences, Packmol keywords, relative documentation links, and scientific terms. The confirmed security-relevant behavior is limited to local helper scripts that write user-selected files and optionally run the local packmol binary without a shell.

## Stats

- - Views: 281
- - Downloads: 9
- - Favorites: 0
- - Popularity score: 0