Packmol — Mixture/Solution Box Generation

When to Use

• User needs to build a liquid simulation box (water, organic solvents)
• User wants to create a mixture of different molecules
• User needs to solvate a solute in a solvent box
• User is preparing initial structures for LAMMPS ReaxFF or classical MD
• User needs to fill a region with molecules at a target density

Prerequisites

1. Packmol installed (packmol < /dev/null should print version)
2. Molecule coordinate files in PDB or XYZ format
3. For molecules from SMILES: first convert with Open Babel (data/openbabel/SKILL.md)

Workflow Steps

1. Prepare molecule files

If starting from SMILES, convert to PDB first:

obabel -:"O" -O water.pdb --gen3d -h
obabel -:"CCO" -O ethanol.pdb --gen3d -h

2. Create Packmol input and run

catgo_workflow_engine(action="add_task", params={
  "workflow_id": "wf_xxx",
  "task_type": "shell",
  "name": "packmol_mix",
  "command": "packmol < mixture.inp > packmol.log 2>&1",
  "input_files": {
    "mixture.inp": "<packmol input>",
    "water.pdb": "<water coords>",
    "ethanol.pdb": "<ethanol coords>"
  },
  "system_name": "water_ethanol_mix"
})

Packmol Input Template — Simple Liquid Box

tolerance 2.0
filetype pdb
output mixture.pdb

structure water.pdb
  number 1000
  inside box 0.0 0.0 0.0 30.0 30.0 30.0
end structure

Packmol Input Template — Binary Mixture

tolerance 2.0
filetype pdb
output mixture.pdb

# Water (70% by count)
structure water.pdb
  number 700
  inside box 0.0 0.0 0.0 40.0 40.0 40.0
end structure

# Ethanol (30% by count)
structure ethanol.pdb
  number 300
  inside box 0.0 0.0 0.0 40.0 40.0 40.0
end structure

Packmol Input Template — Solvated Solute

tolerance 2.0
filetype pdb
output solvated.pdb

# Solute (fixed at center)
structure solute.pdb
  number 1
  center
  fixed 20.0 20.0 20.0 0.0 0.0 0.0
end structure

# Solvent around solute
structure water.pdb
  number 500
  inside box 0.0 0.0 0.0 40.0 40.0 40.0
  outside sphere 20.0 20.0 20.0 5.0
end structure

Packmol Input Template — Layered System (e.g., Interface)

tolerance 2.0
filetype pdb
output interface.pdb

# Liquid phase
structure hexane.pdb
  number 200
  inside box 0.0 0.0 0.0 30.0 30.0 15.0
end structure

# Gas phase
structure oxygen.pdb
  number 50
  inside box 0.0 0.0 15.0 30.0 30.0 30.0
end structure

Box Size Estimation

Target density determines box size. For water at 1 g/cm3:

N_molecules * M_molecule / (N_A * V_box) = density

For 1000 water molecules:
V = 1000 * 18.015 / (6.022e23 * 1.0) = 2.993e-20 cm3
L = V^(1/3) = 3.1e-7 cm = 31.0 Angstrom

Use a box slightly larger (e.g., 32 Ang) and equilibrate with NPT MD.

Parameter Guidance

Parameter	Typical value	Notes
tolerance	2.0 Ang	Minimum distance between atoms of different molecules
filetype	pdb or xyz	Must match input molecule files
number	varies	Number of molecules of each type
inside box	x0 y0 z0 x1 y1 z1	Rectangular region (Angstrom)
inside sphere	cx cy cz r	Spherical region
outside sphere	cx cy cz r	Exclusion zone (for solvation)
fixed	x y z a b c	Fix position and orientation (angles in degrees)

Common Pitfalls

1. Tolerance too small — tolerance 2.0 works for most cases. Smaller values cause Packmol to fail to converge.
2. Box too small — if density is too high, Packmol cannot place all molecules. Increase box size.
3. Wrong filetype — filetype pdb must match the actual input file format.
4. No equilibration after Packmol — Packmol output is NOT equilibrated. Always run NPT MD to relax the density.
5. Missing hydrogens — ensure input molecules have correct hydrogens before packing.
6. Molecule overlap with solute — use outside sphere to prevent solvent from overlapping with a fixed solute.
7. Convergence failure — if Packmol does not converge, increase tolerance or box size, or reduce molecule count.