fixed: distance for initial box was not set by default

If the distance was not given explicitly as setup.distance, the default distance from
equil.DIST was not chosen. Note that the DIST[water] default was set to 1.0 again (instead
of 1.2) because for right now we want to be consistent with the SAMPL5 simulations.
We might set it to 1.2 later (to reduce problems with cutoffs in the box for small molecules)

mdpow/equil.py

@@ -55,8 +55,10 @@
 # BOX <-- forcefields.get_solvent_model(id).coordinates
 
 
+# TODO: change to water distance 1.2 in the future (1.0 for
+#       compatibility with our SAMPL5 runs)
 #: minimum distance between solute and box surface (in nm)
-DIST = {'water': 1.2, 'octanol': 1.5,'cyclohexane':1.5}
+DIST = {'water': 1.0, 'octanol': 1.5, 'cyclohexane': 1.5}
 
 
 class Simulation(Journalled):
@@ -186,7 +188,8 @@ def __init__(self, molecule=None, **kwargs):
                 raise ValueError(msg)
             self.solventmodel = forcefields.get_solvent_model(self.solventmodel_identifier)
 
-            distance = kwargs.pop('distance', DIST[solvent])
+            distance = kwargs.pop('distance', None)
+            distance = distance if distance is not None else DIST[solvent]
 
             self.solvent = AttributeDict(itp=self.solventmodel.itp,
                                          box=self.solventmodel.coordinates,

mdpow/run.py

@@ -203,7 +203,7 @@ def equilibrium_simulation(cfg, solvent, **kwargs):
         # custom mdp files
         mdpfiles = get_mdp_files(cfg, Simulation.protocols)
         try:
-            distance = cfg.get('setup','distance')
+            distance = cfg.get('setup', 'distance')
         except KeyError:
             distance = None # if no distance is specified, None = default