Removing CGAL dependence
Modifications to support RMSD calculations, removing classes we aren't using.
More attempts to get SMIPD to themostat properly
Added large quantities of code for convex hull and constant pressure langevin dynamics.
Added files to module section of Makefile.
updating configure process
Fixed nesting bug in USE_CGAL and USE_QHULL.
Check CGAL and qhull defines
Many fixes for Charmm-type torsions.
Changes to Build system.
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