--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/28 19:33:37	435
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/03/31 21:50:59	438
@@ -314,6 +314,7 @@ void SimSetup::createSim( void ){
     
     if(mol2proc[i] == worldRank ){
       the_molecules[molIndex].setStampID( molCompType[i] );
+      the_molecules[molIndex].setMyIndex( molIndex );
       molIndex++;
     }
   }
@@ -324,6 +325,7 @@ void SimSetup::createSim( void ){
   for(i=0; i<n_components; i++){
     for(j=0; j<components_nmol[i]; j++ ){
       the_molecules[molIndex].setStampID( i );
+      the_molecules[molIndex].setMyIndex( molIndex );
       molIndex++;
     }
   }
@@ -340,7 +342,7 @@ void SimSetup::createSim( void ){
     the_excludes = new Exclude*[simnfo->n_SRI];
     for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
     simnfo->globalExcludes = new int;
-    simnfo->n_exclude = tot_SRI;
+    simnfo->n_exclude = simnfo->n_SRI;
   }
   else{
     
@@ -932,6 +934,8 @@ void SimSetup::makeMolecules( void ){
 
 
     the_molecules[i].initialize( info );
+
+
     atomOffset += info.nAtoms;
     delete[] theBonds;
     delete[] theBends;