packmol

Generate initial molecular configurations for MD simulations using Packmol.

181|20|Updated Apr 29, 2026

Search Tags:#pdb #packmol #solvation #xyz #mixtures #molecular-simulations #liquid-box

Ready to run

npx skills add https://github.com/Hello-QM/catgo-LRG --skill packmol-hello-qm

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: packmol
Source: https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol
Command: npx skills add https://github.com/Hello-QM/catgo-LRG --skill packmol-hello-qm

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Packmol enables automatic generation of initial molecular configurations for MD simulations by packing molecules into defined regions, saving manual setup time.

Core Features & Use Cases

Pack molecules into boxes with specified counts and boundaries.
Build liquid boxes, mixtures, solvated systems, and layered interfaces using PDB/XYZ inputs.
Real-world use: generate a water-ethanol box for MD studies or solvate a solute in solvent.

Quick Start

Create a solvated box by packing water.pdb and solute.pdb into a 40x40x40 Å region.

Frequently Asked Questions about packmol

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

FAQPage Schema

How do I generate initial molecular configurations for MD simulations from PDB files?▼

Generating initial molecular configurations for MD simulations from PDB files requires packing molecules into defined regions with specified counts and boundaries. This Skill automates that process using Packmol to build liquid boxes, mixtures, and solvated systems from your PDB or XYZ inputs.

Can I build a solvated liquid box with a specific solute and solvent mixture?▼

Building a solvated liquid box with a specific solute and solvent mixture is supported. You can pack multiple molecule types, such as a solute and water, into a defined cubic region like a 40x40x40 Å box to create the solvated system for your MD studies.

Do I need Packmol installed to pack molecules into a liquid box?▼

Packmol is required to pack molecules into a liquid box. This Skill serves as an automated interface for the Packmol engine, requiring it to be installed in your environment to process input coordinates and generate the packed molecular configurations.

What input formats are supported for creating molecular mixtures and layered interfaces?▼

PDB and XYZ are the supported input coordinate formats for creating molecular mixtures and layered interfaces. Optional SMILES conversion is also available via Open Babel if you need to generate initial 3D coordinates from chemical identifiers before packing.

How do I convert SMILES strings into 3D coordinates for packing into mixtures?▼

Converting SMILES strings into 3D coordinates for packing into mixtures is handled via Open Babel. This optional step generates the initial PDB or XYZ input files required by Packmol to build your specified liquid boxes or solvated systems.