Improve automatical setup for production protocols

[stefdoerr]

Improve automatical setup for production (and maybe equilibration) protocols. Especially when starting production directly from i.e. pdb+prmtop you need to modify a large amount of parameters to get it to work.

We always assume that production will follow equlibration and will use the files produced by acemd but in many cases you might want to start from pre-equilibrated structures even made from other software.

Example:

from htmd.ui import *
from htmd.protocols.production_v6 import Production

pd = Production(_version=3)
pd.runtime = 100
pd.timeunits = 'ns'
pd.acemd.coordinates = 'structure.pdb'
pd.acemd.structure = 'structure.pdb'
pd.acemd.parameters = 'structure.prmtop'
pd.acemd.bincoordinates = None
pd.acemd.boxsize = '100.35 54.325 168.2823'
pd.acemd.extendedsystem = None
pd.acemd.parmfile = 'structure.prmtop'
pd.write('./equil_finished/', './prod/')

It should really be much simpler than that