IndexError complex_coordinates

[pgrinaway]

When running yank.py example "p-xylene," an IndexError is thrown when yank.py attempts to access self.complex_coordinates[0].

It seems to be related to the following comment at the top of the code:

• Handle complex_coordinates argument in Yank more intelligently if different kinds of input are provided.
  Currently crashes if a Quantity is provided rather than a list of coordinate sets.

I'll play around with it.

[jchodera]

I've added the examples/ directory to yank/yank/ and created a testrun.tcsh launcher script. I also removed the (broken) partial explicit solvent support, since we'll support this in a different manner going forward.

Give this a try and see if it works!

[pgrinaway]

I think this is fixed. I'm going to close this.