Dear all,
I keep having a problem that only for a particular protein the simulation
"freezes" and by freeze I mean, it looks like the job is running but no
changes are made on the output files even if you wait 2 days. I am using
igb=5 on GPU, it is a 114 amino acid long protein, I have the homologous
structure running (112 amino acid long) without a problem. But that specific
one stops without being dropped of the queue or any error messages at all. I
checked the output files, no '*' or 'NaN' are present. I also tried running
on different machines, same thing happens. I tried starting from a different
restart file, nothing changes. I always freezes although at different time
steps.
Has anyone have such a problem before? What can be the causes? I'd
appreciate any comments or suggestions.
Thanks,
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644
Email: korkmaz.wisc.edu
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Received on Fri Oct 14 2011 - 11:00:03 PDT
