Reciprocal-space force group and exclusion corrections

What it does

With Ewald, PME or LJPME, the reciprocal-space sum can be computed in a separate force group by calling setReciprocalSpaceForceGroup, as in OpenMM’s openmm.NonbondedForce. A multiple time-step integrator can then evaluate the reciprocal-space sum, which varies slowly, less often than the direct-space interactions.

The reciprocal-space sum implicitly includes the interactions of excluded pairs and exceptions, and the terms that subtract them are, by default, computed in the direct-space force group, as NonbondedForce does. Since these terms only cancel part of the reciprocal-space sum, they should be integrated along with it whenever the two groups are evaluated at different times; otherwise, the cancellation is incomplete and the slow force acquires a fast, intramolecular component [4, 5]. Calling setReciprocalExclusions(True) moves these terms to the reciprocal-space force group.

Setting it up

force.setNonbondedMethod(nbs.SlicedNonbondedForce.PME)
force.setForceGroup(1)                   # direct space
force.setReciprocalSpaceForceGroup(2)    # reciprocal space
force.setReciprocalExclusions(True)      # and the exclusion corrections with it

Restrictions

• setReciprocalExclusions only matters with Ewald, PME or LJPME, when the reciprocal-space force group differs from the direct-space one. The default, False, keeps the behavior of NonbondedForce.

• By default, turning off direct space with setIncludeDirectSpace(False) also removes the exclusion corrections, as in NonbondedForce. With setReciprocalExclusions(True), they are kept, so a replacement for the direct-space calculation, such as a openmm.CustomNonbondedForce, must then not include them, or they are counted twice.