openmm_solvation

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

Solvate solute Topology using OpenMM’s Modeller.

Parameters:

• solute_topology (openff.toolkit.Topology) – The Topology of the solute to solvate.

• solvent_offmol (openff.toolkit.Molecule) – An OpenFF Molecule representing the solvent species.

• solvation_settings (InterchangeOpenMMSolvationSettings) – Settings defining how the system will be solvated.

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

• ion_concentration (openff.unit.Quantity) – The concentration of NaCl to add to the system when neutralizing. Note that this is ignored if neutralize is False. Must be compatible with mole / liter. Note that this method, unlike the packmol interchange, uses the add neutralize method rather than SLTCAP.

Raises:

ValueError –

• If neutralizing with a non-waterr solvent. * If ion_concentration is not compatible with mole / liter * If neutralize is False and the system has a net charge.