Added notice on need for WHOLEMOLECULE

src/vatom/COM.cpp

@@ -39,6 +39,11 @@ an atom list through the label for the COM action that creates it.
 
 For arbitrary weights (e.g. geometric center) see \ref CENTER.
 
+When running with periodic boundary conditions, the user should take care 
+that the atoms in the COM group actually are in the proper periodic image.
+This is typically achieved using the \ref WHOLEMOLECULE action
+before COM calculation.
+
 \par Examples
 
 The following input instructs plumed to print the distance between the

src/vatom/Center.cpp

@@ -40,6 +40,11 @@ Notice that the generated virtual atom has charge equal to the sum of the
 charges and mass equal to the sum of the masses. If used with the MASS flag,
 then it provides a result identical to \ref COM.
 
+When running with periodic boundary conditions, the user should take care 
+that the atoms in the COM group actually are in the proper periodic image.
+This is typically achieved using the \ref WHOLEMOLECULE action
+before COM calculation.
+
 \par Examples
 
 \verbatim