Fix the handling and units of box lengths (they are not independent from

boxVectors, so they should be a property computed from the vectors). Also make
sure that any attempts to change the boxVectors correspondingly deletes the
cached copies of the box lengths so they are recomputed if necessary.

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

@@ -755,6 +755,12 @@ class CharmmPsfFile(object):
             - alpha, beta, gamma (floats, optional) : Angles between the
                 periodic cells.
         """
+        try:
+            # Since we are setting the box, delete the cached box lengths if we
+            # have them to make sure they are recomputed if desired.
+            del self._boxLengths
+        except AttributeError:
+            pass
         self.box_vectors = _box_vectors_from_lengths_angles(a, b, c,
                                                             alpha, beta, gamma)
         # If we already have a _topology instance, then we have possibly changed
@@ -1422,9 +1428,30 @@ class CharmmPsfFile(object):
     @property
     def boxLengths(self):
         """ Return tuple of 3 units """
+        try:
+            # See if we have a cached version
+            return self._boxLengths
+        except AttributeError:
+            pass
         if self.box_vectors is not None:
-            return (self.box_vectors[0][0], self.box_vectors[0][1],
-                    self.box_vectors[0][2])
+            # Get the lengths of each vector
+            if u.is_quantity(self.box_vectors):
+                # Unlikely -- each vector is like a quantity
+                vecs = self.box_vectors.value_in_unit(u.nanometers)
+            elif u.is_quantity(self.box_vectors[0]):
+                # Assume all box vectors are quantities
+                vecs = [x.value_in_unit(u.nanometers) for x in self.box_vectors]
+            else:
+                # Assume nanometers
+                vecs = self.box_vectors
+            a = sqrt(vecs[0][0]*vecs[0][0] + vecs[0][1]*vecs[0][1] +
+                     vecs[0][2]*vecs[0][2])
+            b = sqrt(vecs[1][0]*vecs[1][0] + vecs[1][1]*vecs[1][1] +
+                     vecs[1][2]*vecs[1][2])
+            c = sqrt(vecs[2][0]*vecs[2][0] + vecs[2][1]*vecs[2][1] +
+                     vecs[2][2]*vecs[2][2])
+            self._boxLengths = (a, b, c) * u.nanometers
+            return self._boxLengths
         return None
 
     @boxLengths.setter
@@ -1440,6 +1467,12 @@ class CharmmPsfFile(object):
     @boxVectors.setter
     def boxVectors(self, stuff):
         """ Sets the box vectors """
+        try:
+            # We may be changing the box, so delete the cached box lengths to
+            # make sure they are recomputed if desired
+            del self._boxLengths
+        except AttributeError:
+            pass
         self.box_vectors = stuff
 
     def deleteCmap(self):