Packmol

Packmol

Overview

Packmol is a tool for building initial configurations of molecular systems by packing molecules subject to geometric constraints. It is commonly used as a pre-processing step for molecular dynamics (MD) simulations.

When to Use Packmol vs. Other Tools

| Scenario | Recommended Tool | Why | |---|---|---| | Solvating a solute, building bulk mixtures, or creating droplets/slabs for MD | Packmol | Purpose-built for packing with geometric constraints | | Building crystalline supercells or surfaces from unit cells | ASE / pymatgen | Better support for periodic symmetry and space groups | | Generating polymer chains or highly branched topologies | polymer-build / custom scripts | Packmol requires pre-built monomer structures as inputs |

Key rule: Use Packmol when you need to combine pre-existing molecular structures into an initial MD configuration with control over spatial placement and density.

Requirements

Packmol must be installed and the packmol binary available in PATH. The repo includes local references for syntax, examples, and troubleshooting.

Core Capabilities

1. Draft and Validate Inputs

Use local references to write correct input files:

• references/syntax.md — Complete keyword reference, nesting rules, and unit conventions.
• references/examples.md — Copy-pasteable patterns for bulk mixtures, solvated solutes, droplets, slabs, and multi-region systems.
• references/troubleshooting.md — Common errors, convergence issues, and quick sanity-check heuristics.

2. Run Packmol

packmol  1e-3" | Poor convergence | Increase box size, loosen `tolerance`, change `seed`, or increase `nloop` / `maxit` |
| "The structure file could not be opened" | Wrong relative path or missing file | Verify paths and working directory |
| "Number of atoms in structure file ..." | `filetype` mismatches actual format | Correct `filetype` to match `pdb`, `xyz`, or `mol2` |
| "Inconsistent constraints" | Contradictory `inside` / `outside` directives | Ensure boundaries are separated by more than `tolerance` |
| Very slow optimization | Over-constrained or near-critical packing | Increase volume margin or slightly loosen `tolerance` |

## References

- **Official Website / Manual**: http://m3g.iqm.unicamp.br/packmol/home.shtml
- **GitHub**: https://github.com/m3g/packmol
- **Local Syntax Guide**: `references/syntax.md`
- **Local Examples**: `references/examples.md`
- **Local Troubleshooting**: `references/troubleshooting.md`

## Getting Live Information

If the user asks about recently added features, new options, or version-specific syntax changes, use `WebFetch` on the official documentation at http://m3g.iqm.unicamp.br/packmol/home.shtml before answering.

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [WuGroup-XJTLU](https://github.com/WuGroup-XJTLU)
- **Source:** [WuGroup-XJTLU/cc-skills-ZhenghaoWu-Group](https://github.com/WuGroup-XJTLU/cc-skills-ZhenghaoWu-Group)
- **License:** Apache-2.0

Install and usage instructions live in the source repository linked above.