leeping/forcebalance — pull request #29 by leeping (2013-10-18 09:46:35+00:00)
Title: 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!