Tweaks to timed run_type option
Tweaks to timed run_type option

timed option does not calculate free energies if replica exchange
cycles have not complete. An error was fixed wit the equilibrated state.

luizcieslak/AlGDock,gkumar7/AlGDock,CCBatIIT/AlGDock,CCBatIIT/AlGDock,CCBatIIT/AlGDock,luizcieslak/AlGDock,gkumar7/AlGDock,CCBatIIT/AlGDock,gkumar7/AlGDock,gkumar7/AlGDock,luizcieslak/AlGDock,luizcieslak/AlGDock