[Thermo] Merge md() and molecular_dynamics() methods

[leeping]

Currently the molecular_dynamics() method (implemented by me) returns a few specific pieces of information, such as the time series of energies, densities and so on. This wasn't general enough for the Thermo target so md() was added by Erik. At some point I would like to merge the two, and create a more general method for running molecular dynamics simulations + returning properties.

[leeping]

Also mostly duplicated: gmxprefix.bash and rungmx.sh

[leeping]

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.