--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/12 20:32:20	1097
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/13 16:26:03	1104
@@ -167,7 +167,7 @@ void SimSetup::makeMolecules(void){
 
 void SimSetup::makeMolecules(void){
   int i, j, k;
-  int exI, exJ, exK, exL, slI;
+  int exI, exJ, exK, exL, slI, slJ;
   int tempI, tempJ, tempK, tempL;
   int molI;
   int stampID, atomOffset, rbOffset;
@@ -465,7 +465,40 @@ void SimSetup::makeMolecules(void){
             
           }
         }
+
+        molInfo.myRigidBodies.push_back(myRB);
+        info[k].rigidBodies.push_back(myRB);
+      }
+      
+
+      // After this is all set up, scan through the atoms to 
+      // see if they can be added to the integrableObjects:
+
+      for (j = 0; j < molInfo.nAtoms; j++){
+
+#ifdef IS_MPI
+        slJ = molInfo.myAtoms[j]->getGlobalIndex();
+#else
+        slJ = j+atomOffset;
+#endif
+
+        // if they aren't on the skip list, then they can be integrated
+
+        if (skipList.find(slJ) == skipList.end()) {
+          mySD = (StuntDouble *) molInfo.myAtoms[j];
+          info[k].integrableObjects.push_back(mySD);
+          molInfo.myIntegrableObjects.push_back(mySD);
+        }
+      }
+
+      // all rigid bodies are integrated:
+
+      for (j = 0; j < molInfo.nRigidBodies; j++) {
+        mySD = (StuntDouble *) molInfo.myRigidBodies[j];
+        info[k].integrableObjects.push_back(mySD);      
+        molInfo.myIntegrableObjects.push_back(mySD);
       }
+    
       
       // send the arrays off to the forceField for init.
       
@@ -482,28 +515,7 @@ void SimSetup::makeMolecules(void){
       delete[] theBonds;
       delete[] theBends;
       delete[] theTorsions;
-    }
-
-    // build up the integrableObjects vector:
-
-    for (i = 0; i < info[k].n_atoms; i++) {
-      
-#ifdef IS_MPI
-      slI = info[k].atoms[i]->getGlobalIndex();
-#else
-      slI = i;
-#endif
-
-      if (skipList.find(slI) == skipList.end()) {
-        mySD = (StuntDouble *) info[k].atoms[i];
-        info[k].integrableObjects.push_back(mySD);
-      }
-    }
-    for (i = 0; i < info[k].rigidBodies.size(); i++) {
-      mySD = (StuntDouble *) info[k].rigidBodies[i];
-      info[k].integrableObjects.push_back(mySD);      
-    }
-    
+    }    
   }
 
 #ifdef IS_MPI