Dexter,
What exactly do you think is a long running molecule anyway?
In my experience over the past few months, it is not unusual for a single work unit to take an entire day to run. In fact the one that is running now on my laptop is at 36 hours.
More often than not a work unit will take more than 12 hours than less than 4 hours.
Your problem seems to do with not being able to leave the computer running, and losing valuable processing time.
Here are some tips you should consider.
1) Run UD Monitor: this will tell you how long it has been since your last save, as well as backup your jobs, so you can recover them if you crash or have to shut down
2) Let it run overnight: I find it hard to believe that someone needs to use the computer 24/7. Even so, the agent is pretty unobtrusive, and only uses whatever processing power that your computer can spare
3) Don't worry so much about how long a job takes. The longer the work unit, the more points you will earn. If your pc rates you 15 pts/hour, and you process only 4 hours, you will only get 60 points. If the same job runs for 24 hours, then you would get 360 points.
4) Try to find another computer to run it on. It does not have to be a state of the art P4 or Athon. If you have an older pc sitting around in a closet, attic, basement...wipe off the dust, plug it in and crunch some conformers. It might take a little longer to complete, but it will still do the job.
5) Have some patience, don't be in such a hurry, and brush your teeth before going to bed.
-Tacks
