[Thermo] Merge md() and molecular_dynamics() methods about forcebalance HOT 2 CLOSED

Also mostly duplicated: gmxprefix.bash and rungmx.sh

from forcebalance.

Here's a bit from an email thread, to remind myself:

• Introduced a new method md() in gmxio.py. It is basically the
  same as molecular_dynamics() but does not do the analysis, because
  this will be different for the different quantities.

Cool. This could possibly replace molecular_dynamics() at some
point - I was not completely happy with how it was doing the analysis
since it returns a set of chosen quantities. Related to item (2)
above, it might be helpful for the engine to have methods that
retrieve the time series such as mdtraj_potentials(), mdtraj_rhos()
or something.

from forcebalance.