What revision of AMBER? What GPU? What OS? What driver? What toolkit did
you compile with?
On Fri, Oct 14, 2011 at 10:55 AM, E. Nihal Korkmaz
<enihalkorkmaz.gmail.com>wrote:
> 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 - 11:30:03 PDT
