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.
Merge pull request #469 from swails/fix_charmm_box

Fix the handling and units of box lengths in CHARMM files
Merge pull request #470 from swails/master

Make separate lists for dihedrals and the dihedrals with loaded parameters.
Fixed bug when multiple virtual sites depend on the same particles (see bug 2019)
Merge pull request #471 from peastman/master

Fixed bug when multiple virtual sites depend on the same particles (see bug 2019)
Where did this input.inpcrd file come from?  There was an extra space between
the 3rd and 4th columns, making it an invalid Amber inpcrd file (which the new
parser cannot handle).