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, compared to before where all of the system calls were contained in the Target classes.  The goal is to increase the reusability 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!