Fixed problem w/ setting of bond offsets

plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaGpu.cpp

@@ -1125,12 +1125,13 @@ void gpuSetAmoebaBondOffsets(amoebaGpuContext amoebaGpu )
 {
  
     // make sure only flip once
-
+/*
     static int flipped = 0;
     if( amoebaGpu && flipped ){
         return;
     }
     flipped = 1;
+*/
     _gpuContext* gpu                                           = amoebaGpu->gpuContext;
 
     amoebaGpu->amoebaSim.amoebaBond_offset                     = amoebaGpu->psAmoebaBondParameter ? amoebaGpu->psAmoebaBondParameter->_stride : 0;
@@ -1270,7 +1271,6 @@ void gpuSetAmoebaBondOffsets(amoebaGpuContext amoebaGpu )
         }
 
     }
-
 }
 
 /**---------------------------------------------------------------------------------------

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedAndGkFields.cu

@@ -292,7 +292,7 @@ void kReduceMutualInducedAndGkFieldDelta_kernel( float* arrayOfDeltas1, float* a
 
     // load deltas
 
-    while( pos <  3*cAmoebaSim.numberOfAtoms )
+    while( pos < 3*cAmoebaSim.numberOfAtoms )
     {   
         delta[threadIdx.x].x  += arrayOfDeltas1[pos];
         delta[threadIdx.x].y  += arrayOfDeltas2[pos];

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaRotateFrame.cu

@@ -677,9 +677,13 @@ void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaG
     // calculate electrostatic forces
 
     if( amoebaGpu->multipoleNonbondedMethod == AMOEBA_NO_CUTOFF ){
+
         cudaComputeAmoebaElectrostatic( amoebaGpu );
+
         // map torques to forces
+
         cudaComputeAmoebaMapTorquesAndAddTotalForce( amoebaGpu, amoebaGpu->psTorque, amoebaGpu->psForce, amoebaGpu->gpuContext->psForce4 );
+
     } else {
         cudaComputeAmoebaPmeElectrostatic( amoebaGpu );
     }