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Chenghao-Wu
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packmol

Generate Packmol input files for molecular packing tasks with constraints.

Updated Jan 3, 2026
Search Tags:#packmol#molecular-packing#md-input#solvation#protein-solvation#interface-packing
One-click install
npx skills add https://github.com/Chenghao-Wu/skill_packmol --skill packmol
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: packmol
Source: https://github.com/Chenghao-Wu/skill_packmol/tree/main/.claude/skills/packmol
Command: npx skills add https://github.com/Chenghao-Wu/skill_packmol --skill packmol

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

Packmol input generation for molecular packing tasks is tedious and error-prone; this skill automates the creation of input files that define molecular counts, constraints, and positioning for MD-ready configurations.

Core Features & Use Cases

  • Generate Packmol inputs for simple boxes, solvated proteins, and interfacial systems.
  • Validate inputs and offer structured workflows that streamline setup for MD workflows.
  • Support common constraints (box, sphere, plane) and multi-component mixtures.

Quick Start

Describe your packing goal in natural language, and Claude Code will generate a Packmol input that packs your molecules with the correct constraints.

Frequently Asked Questions about packmol

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate a Packmol input file for solvating a protein?▼

You can generate a Packmol input file for protein solvation by describing your packing goal in natural language, which produces a valid input file with correct tolerance, filetype, output, and structure blocks for molecular placement.

Can I create Packmol inputs for multi-component mixtures and interfacial systems?▼

Yes, Packmol inputs for multi-component mixtures and interfacial systems are generated by specifying your constraints in natural language, and the skill applies them to produce inputs for boxes, interfaces, and solvated proteins.

What types of constraints are supported when packing molecules for MD setups?▼

Supported constraints for packing molecules for MD setups include box, sphere, and plane constraints, which define molecular counts and positioning for multi-component mixtures in MD-ready configurations.

How do I validate a Packmol input file before running molecular dynamics simulations?▼

You can validate a Packmol input file before running molecular dynamics simulations using the skill's optional validation steps, which ensure the generated input is correctly formed and ready for Packmol execution.

Why does my Packmol packing task keep failing due to incorrect structure blocks?▼

Packmol packing tasks frequently fail due to incorrectly formed structure, tolerance, or filetype blocks, which this skill resolves by automatically generating a valid input file with correctly structured constraints for MD-ready configurations.

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