System should not be converted to use ONLY the perturbed free energies.
This should be a much faster process than previously since the mbar
object does not have to be recreated each time.
Removed most the active debug tracer lines. No syntax errors found, will
need real data to test a full run.
I have timing things in the mbar creation step, but those have been
commented out now. The script should function fine, need real data
though.