Agent skill · research science · aiskillstore
packmol
This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular dynamics", or discusses molecular packing, solvation, or building simulation starting structures.
Why this skill is useful
Provides specific input file structures and commands for using Packmol that the AI wouldn't reliably generate on its own.
What it needs
Requires packmol installed locally. About 6k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
Packmol Skill Build initial configurations for molecular dynamics simulations using Packmol. What is Packmol? Packmol creates initial configurations for MD simulations by packing molecules according to spatial constraints. It places molecules in boxes, around proteins, at interfaces, or within complex geometries (spheres, cylinders, ellipsoids) while ensuring no overlaps. Installation Install Packmol via pip: Verify installation: For more installation options, see the Packmol website. Quick Start Basic Box Packing Create a simple box of water molecules: Run Packmol: Solvate a Protein Solvate a protein with water and ions: Liquid-Liquid Interface Build a water/chloroform interface: Core Concepts Input File Structure Every Packmol input file requires: 1. tolerance: Minimum distance between atoms (Å) 2. output: Output filename 3. filetype: Format (pdb, xyz, tinker) 4. structure blocks: Define molecules to place Structure Block Syntax Common Constraint Types box: inside box xmin ymin zmin xmax ymax zmax sphere: inside sphere xcenter ycenter zcenter radius cylinder: inside cylinder x1 y1 z1 dx dy dz radius length plane: above plane a b c d or below plane a b c d ellipsoid: inside ellipsoid xc yc zc xa yb zc scale See references/constraints.md for complete constraint documentation. Workflows 1. Basic Molecular Packing Build boxes with multiple molecule types. Example: Water/ethanol mixture 2. Protein Solvation Solvate biomolecules with water and ions for neutralization. Key parameters: Use fixed with center for the protein Add Na+/Cl- ions for neutrality and concentration Calculate box size based on protein + solvent shell Automatic solvation helper: 3. Interface Systems Build liquid-liquid or liquid-vapor interfaces using plane constraints. Example: Water/hexane interface 4. Advanced Constraints Use spherical, cylindrical, or ellipsoidal constraints for complex geometries. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/packmol