packmol_solvation

pontibus.utils.system_solvation.packmol_solvation(solute_topology: Topology, solvent_offmol: Molecule, solvation_settings: PackmolSolvationSettings, neutralize: bool, ion_concentration: Quantity) → Topology

Solvate solute Topology using the Interchange packmol interface.

Parameters:

• solute_topology (Topology) – The solute Topology to solvate.

• solvent_offmol (OFFMolecule) – An OpenFF Molecule representing the solvent.

• solvation_settings (PackmolSolvationSettings) – Settings for how to solvate the system using the packmol interface.

• neutralize (bool) – Whether or not the system should be neutralized.

• ion_concentration (Quantity) – The concentration of NaCl to add to the system when neutralizing. Note that this is ignored if neutralize if False. Must be compatible with mole / liter. Addition of ions is done through the SLTCAP method.

Returns:

The solvated Topology.

Return type:

Topology

Raises:

ValueError – If neutralize is True and solvent_offmol is not water. if ion_concentration is not compatible with mole / liter.