Finish the last commit. Make sure the box vector calculation from the lengths

and angles makes numbers exactly 0 that _should_ be zero (but aren't due to
precision and round-off issues).

Now the box vector code in the prmtop file is fully general for every type of
box that Amber supports.

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

@@ -141,7 +141,8 @@ class AmberPrmtopFile(object):
         # Set the periodic box size.
 
         if prmtop.getIfBox():
-            top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer)
+            conv = (1.0 * unit.angstrom).value_in_unit(unit.nanometer)
+            top.setUnitCellDimensions(tuple(x*conv for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer)
 
     def createSystem(self, nonbondedMethod=ff.NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
                      constraints=None, rigidWater=True, implicitSolvent=None,

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -742,10 +742,9 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
         _box_vectors_from_lengths_angles([boxX, boxY, boxZ],
                                          [boxBeta, boxBeta, boxBeta],
                                          tmp)
-        d0 = units.Quantity(0.0, units.angstroms)
-        xVec = units.Quantity(tmp[0], u.angstroms)
-        yVec = units.Quantity(tmp[1], u.angstroms)
-        zVec = units.Quantity(tmp[2], u.angstroms)
+        xVec = units.Quantity(tmp[0], units.angstroms)
+        yVec = units.Quantity(tmp[1], units.angstroms)
+        zVec = units.Quantity(tmp[2], units.angstroms)
         system.setDefaultPeriodicBoxVectors(xVec, yVec, zVec)
 
         # Set cutoff.
@@ -1235,6 +1234,12 @@ def _box_vectors_from_lengths_angles(lengths, angles, boxVectors):
 
     boxVectors[0][1] = boxVectors[0][2] = boxVectors[1][2] = 0.0
 
+    # Now make sure any vector close to zero is zero exactly
+    for i in range(3):
+        for j in range(3):
+            if abs(boxVectors[i][j]) < TINY:
+                boxVectors[i][j] = 0.0
+
 def readAmberCoordinates(filename, asNumpy=False):
     """
     Read atomic coordinates (and optionally, box vectors) from Amber formatted coordinate file.