--- trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/15 16:18:26	1113
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/27 16:26:44	1136
@@ -42,7 +42,8 @@ void Molecule::initialize( molInit &theInit ){
 
 
 void Molecule::initialize( molInit &theInit ){
-
+  double totMass;
+  
   nAtoms = theInit.nAtoms;
   nMembers = nAtoms;
   nBonds = theInit.nBonds;
@@ -61,17 +62,30 @@ void Molecule::initialize( molInit &theInit ){
 
   for (int i = 0; i < myRigidBodies.size(); i++) 
       myRigidBodies[i]->calcRefCoords();
-    
+
+
+  //the mass ratio will never change during the simulation. Thus, we could
+  //just calculate it at the begining of the simulation
+  totMass = getTotalMass();
+  for(int i = 0; i < nAtoms; i ++)
+    myAtoms[i]->setMassRatio(myAtoms[i]->getMass()/totMass);  
 }
 
 void Molecule::calcForces( void ){
   
   int i;
+  double com[3];
 
   for(i=0; i<myRigidBodies.size(); i++) {
     myRigidBodies[i]->updateAtoms();
   }
 
+  //calculate the center of mass of the molecule
+  getCOM(com);  
+  for(int i = 0; i < nAtoms; i ++)
+    myAtoms[i]->setRc(com);  
+  
+
   for(i=0; i<nBonds; i++){
     myBonds[i]->calc_forces();
   }