NonbondedForce sometimes included energy terms that weren't appropriate to the...

NonbondedForce sometimes included energy terms that weren't appropriate to the specified force groups

platforms/reference/src/ReferenceKernels.cpp

@@ -704,10 +704,10 @@ double ReferenceCalcNonbondedForceKernel::execute(ContextImpl& context, bool inc
         ReferenceBondForce refBondForce;
         ReferenceLJCoulomb14 nonbonded14;
         refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
-    }
-    if (periodic || ewald || pme) {
-        RealVec& boxSize = extractBoxSize(context);
-        energy += dispersionCoefficient/(boxSize[0]*boxSize[1]*boxSize[2]);
+        if (periodic || ewald || pme) {
+            RealVec& boxSize = extractBoxSize(context);
+            energy += dispersionCoefficient/(boxSize[0]*boxSize[1]*boxSize[2]);
+        }
     }
     return energy;
 }

platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp

@@ -196,12 +196,13 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
 // SELF ENERGY
 // **************************************************************************************
 
-    for( int atomID = 0; atomID < numberOfAtoms; atomID++ ){
-        RealOpenMM selfEwaldEnergy       = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[atomID][QIndex]*atomParameters[atomID][QIndex] * alphaEwald/SQRT_PI);
-        totalSelfEwaldEnergy            -= selfEwaldEnergy;
-
-        if( energyByAtom ){
-           energyByAtom[atomID]         -= selfEwaldEnergy;
+    if (includeReciprocal) {
+        for( int atomID = 0; atomID < numberOfAtoms; atomID++ ){
+            RealOpenMM selfEwaldEnergy       = (RealOpenMM) (ONE_4PI_EPS0*atomParameters[atomID][QIndex]*atomParameters[atomID][QIndex] * alphaEwald/SQRT_PI);
+            totalSelfEwaldEnergy            -= selfEwaldEnergy;
+            if( energyByAtom ){
+                energyByAtom[atomID]        -= selfEwaldEnergy;
+            }
         }
     }