openmmtools.forcefactories.replace_reaction_field

openmmtools.forcefactories.replace_reaction_field(reference_system, switch_width=Quantity(value=1.0, unit=angstrom), return_copy=True, shifted=False)

Return a system converted to use a switched reaction-field electrostatics using openmmtools.forces.UnshiftedReactionField.

This will add an UnshiftedReactionFieldForce or SwitchedReactionFieldForce for each NonbondedForce that utilizes CutoffPeriodic.

Note that AbsoluteAlchemicalFactory.create_alchemical_system() can NOT handle the resulting System object yet since the CustomNonbondedForce are not recognized and re-coded.

Parameters:

reference_system : simtk.openmm.System

The system to use as a reference. This will be modified only if return_copy is False.

switch_width : simtk.unit.Quantity, default=1.0*angstrom

Switch width for electrostatics (units of distance).

return_copy : bool, optional, default=True

If True, reference_system is not modified, and a copy is returned. Setting it to False speeds up the function execution but modifies the reference_system object.

shifted : bool, optional, default=False

If True, a shifted reaction-field will be used.

Returns:

system : simtk.openmm.System

System with reaction-field converted to c_rf = 0