--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/14 15:37:41	1108
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/15 16:18:26	1113
@@ -147,13 +147,6 @@ void SimSetup::createSim(void){
   // make the output filenames
 
   makeOutNames();
-
-  if (globals->haveMinimizer())
-    // make minimizer
-    makeMinimizer();
-  else
-    // make the integrator
-    makeIntegrator();
   
 #ifdef IS_MPI
   mpiSim->mpiRefresh();
@@ -162,6 +155,14 @@ void SimSetup::createSim(void){
   // initialize the Fortran
 
   initFortran();
+
+  if (globals->haveMinimizer())
+    // make minimizer
+    makeMinimizer();
+  else
+    // make the integrator
+    makeIntegrator();
+
 }
 
 
@@ -262,10 +263,10 @@ void SimSetup::makeMolecules(void){
         else{
 
           molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
+
         }
 
         molInfo.myAtoms[j]->setType(currentAtom->getType());
-
 #ifdef IS_MPI
 
         molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
@@ -409,6 +410,9 @@ void SimSetup::makeMolecules(void){
         info[k].excludes->addPair(exK, exL);
       }
 
+      
+      molInfo.myRigidBodies.clear();
+      
       for (j = 0; j < molInfo.nRigidBodies; j++){
 
         currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
@@ -418,7 +422,7 @@ void SimSetup::makeMolecules(void){
 
         myRB = new RigidBody();
 
-        sprintf(rbName,"%s_RB_%s", molName, j);
+        sprintf(rbName,"%s_RB_%d", molName, j);
         myRB->setType(rbName);
         
         for (rb1 = 0; rb1 < nMembers; rb1++) {
@@ -479,6 +483,9 @@ void SimSetup::makeMolecules(void){
 
       // After this is all set up, scan through the atoms to 
       // see if they can be added to the integrableObjects:
+
+      molInfo.myIntegrableObjects.clear();
+      
 
       for (j = 0; j < molInfo.nAtoms; j++){
 
@@ -957,6 +964,7 @@ void SimSetup::finalInfoCheck(void){
 void SimSetup::finalInfoCheck(void){
   int index;
   int usesDipoles;
+  int usesCharges;
   int i;
 
   for (i = 0; i < nInfo; i++){
@@ -968,7 +976,12 @@ void SimSetup::finalInfoCheck(void){
       usesDipoles = (info[i].atoms[index])->hasDipole();
       index++;
     }
-
+    index = 0;
+    usesCharges = 0;
+    while ((index < info[i].n_atoms) && !usesCharges){
+      usesCharges= (info[i].atoms[index])->hasCharge();
+      index++;
+    }
 #ifdef IS_MPI
     int myUse = usesDipoles;
     MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
@@ -1019,7 +1032,7 @@ void SimSetup::finalInfoCheck(void){
       info[i].dielectric = globals->getDielectric();
     }
     else{
-      if (usesDipoles){
+      if (usesDipoles || usesCharges){
         if (!globals->haveECR()){
           sprintf(painCave.errMsg,
                   "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"