Revised GromacsStructureParser to use numpy

Allows operations to be performed on arrays, eliminiating
issues with varying the length of the gro files.
Rewrote the GromacsToGromacs.py and input directory structure.
Now, each folder has structure files conf.gro and topology files
topol.top.

Standard call would now be, for example

python GromacsToGromacs.py -n 2PPN