Packmol Interface

Packmol is a powerful tool for creating initial configurations for molecular dynamics simulations by packing molecules into a given region of space. rdkit2ase provides a python interface to Packmol. If you have packmol installed, you can use it via pack create periodic boxes from ase.Atoms objects.

import rdkit2ase

The interface takes

• a list of lists of ase.Atoms objects to be packed,

• the number of each type of molecule, if larger than the number of provided ase.Atoms objects the objects will be duplicated,

• the density of the final box in kg/m³.

You can either specify the path to the Packmol executable, or use a Julia installation with the Packmol package.

water = rdkit2ase.smiles2conformers("O", numConfs=10)
etoh = rdkit2ase.smiles2conformers("CCO", numConfs=10)
box = rdkit2ase.pack(
    data=[water, etoh], counts=[5, 5], density=800, packmol="packmol.jl"
)

print(box)

Atoms(symbols='OH2OH2OH2OH2OH2C2OH6C2OH6C2OH6C2OH6C2OH6', pbc=True, cell=[8.728901107040366, 8.728901107040366, 8.728901107040366], atomtypes=..., bfactor=..., occupancy=..., residuenames=..., residuenumbers=...)

You can utilize all other features here as well.

waters = rdkit2ase.match_substructure(
    box,
    smiles="O",
)
etohs = rdkit2ase.match_substructure(
    box,
    smiles="CCO",
)
print(f"Found {len(waters)} water molecules and {len(etohs)} ethanol molecules.")

Found 5 water molecules and 5 ethanol molecules.