Some updates for restraints and fluctuating charges in Ewald
MERGE OpenMD development branch 1465:1781 into trunk
removing spurious cutoffGroup lines from default water.md sample files
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
Fixed Makefile problems with the samples and added several missing makefiles.
converted samples over to the OOPSE-4 file format Fixed an MPI bug in thermodynamic integration
Added tred to sample water.md files
Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)
Removed sqrt splines and shape stuff (doesn't work, so why was it in there?). Changed some of the water samples to use shifted_force. Probably should set the defaults to use the damped version now that we sped it up.
remove deprecated keywords from samples
added default restraint spring constants into Globals
fixing up some samples
forgot a couple of makefiles
added some samples