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On my X2 3800 w/1Gb of memory I loaded 5.04 and now I'm getting tiny proteins (762 and 771) and damn slow crunching, < 100ppd per instance.
I chose the -advmethods within the config script.
Could this be giving me the small proteins?
I run the -advmethods flag on my X2 folding box and I seem to get a variety of cores all the time. I mostly get gromacs but lately have been getting ambers and doublegromacs stuff to chew on with the occasional GBgromacs. I wouldn't worry about the small stuff with the flag, it will vary all the time.
I've noticed similar behavior on my single core 3500+ in the recent weeks. Lots of 46 and smaller point proteins, and then on the other end of the spectrum, a handful of those absolutely huge multi-day WU's.