To run a test, do the following:
1) Go into the folder
2) ../test.py [gro] [top] [mdp] or run "command.sh"

Notes: Gromacs and OpenMM apply constraints differently.  
So if you have rigid water molecules or constraints, run
it once, and then run it again on the generated "constrained.gro".
Otherwise there will be energy and force differences.

Also: OpenMM auto-sets the PME Fourier grid.  I had to
modify ReferenceKernels.cpp to print the grid out, then
I set the corresponding fourier_n[xyz] in the .mdp file
to make things more consistent between the two codes.

