Moved AbInitio_GMX functionality into new GMX engine.

This begins to address issue #26.

The new GMX engine contains all the system calls to GROMACS, which is a different design compared to before, where all of the system calls were contained in the Target classes.  The goal is to increase the usability of code.

Currently Abinitio_GMX is not eliminated but 95% of the code is repackaged into the GMX engine.  I'm still thinking about how to potentially get rid of this class in the future.

Comments welcome!