Started fixing some samples for OpenMD 2.0 release
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
remove deprecated keywords from samples
fixed up some sample md files
fix Makefile under water directory
add Makefile to sample directory
Import of OOPSE v. 2.0