The initial problem we had has now been cleared up. You both bring up significant points I hope to address.
From what you're saying, I am unsure whether this implementation is parallel or not. Dr. Nilsson, you say that this is run in parallel with a non-parallel CHARMM version. Where should I be looking to verify this?
Dr. Venable, thank for your suggestion regarding simplifying the logfile output. I've done as you suggest, and the logfile is much easier to manage.