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)
remove deprecated keywords from samples
fixing up the samples
fixed some samples
fixing up some samples
Updated tap sample
added a tap example for testing purposes