--- trunk/src/math/RMSD.hpp	2009/04/03 17:44:57	1335
+++ branches/development/src/math/RMSD.hpp	2012/07/06 22:01:58	1767
@@ -38,7 +38,7 @@
 #include "config.h"
 #include "math/SquareMatrix3.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   class RMSD{
   public:
@@ -52,7 +52,7 @@ namespace oopse {
       ref_ = ref;
       ref_com = V3Zero;
       
-      for (int n=0; n<ref_.size(); n++) {
+      for (unsigned int n = 0; n < ref_.size(); n++) {
         ref_com += ref_[n];
       }
       ref_com /= (RealType)ref.size();      
@@ -71,18 +71,18 @@ namespace oopse {
      */
     RealType calculate_rmsd(std::vector<Vector3d> mov,
                             Vector3d mov_com,
-                            Vector3d mov_to_ref,
-                            RotMat3x3d U);
+                            Vector3d mov_to_ref);
     
-
     /* 
      * optimal_superposition()
      *
      *   Returns best-fit rotation matrix 
      */
-    RotMat3x3d optimal_superposition(std::vector<Vector3d> mov);
+    RotMat3x3d optimal_superposition(std::vector<Vector3d> mov,
+                            Vector3d mov_com,
+                            Vector3d mov_to_ref);
 
-
+    
   protected:
     std::vector<Vector3d> ref_;
     Vector3d ref_com;