https://salilab.org/imp/bugs/show_bug.cgi?id=106

--- Comment #2 from drussel@SALILAB.ORG 2010-04-20 12:43:28 PDT --- I see two easy ways forward: 1. convert the bad_alloc into a python-friendly exception with a nicer message. I'm not sure how useful this is as I suspect a general purpose optimizer and 100k particles and a nonbonded list can't be stably mixed with our current setup as it is likely to hit a tight configuration at some point. 2. convert the bad_alloc to a ModelException. Then if MC is being run, it can reject the conformation or CG run and try another so at least something can come out of it. But it makes the assumption that such a configuration would have a bad score.

Slightly more involved, which I used to have in there is to reduce the slack in the NBL and try again. If we have a test bed, then I can experiment with that.