Throw PSF warning only in serious cases

when the number of molecules does not agree
with the number of holders.

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -335,9 +335,12 @@ class CharmmPsfFile(object):
         set_molecules(atom_list)
         molecule_list = [atom.marked for atom in atom_list]
         if len(holder) == len(atom_list):
-            #if molecule_list != holder:
-            #    warnings.warn('Detected PSF molecule section that is WRONG. '
-            #                  'Resetting molecularity.', CharmmPSFWarning)
+            if len(molecule_list) != len(holder):
+                # The MOLNT section is only used for fluctuating charge models,
+                # which are currently not supported anyway.
+                # Therefore, we only check the lengths of the lists now rather than their contents.
+                warnings.warn('Detected PSF molecule section that is WRONG. '
+                              'Resetting molecularity.', CharmmPSFWarning)
             # We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
             numlp, numlph = psfsections['NUMLP NUMLPH'][0]
             if numlp != 0 or numlph != 0: