Errors during equilibration: segmentation fault and bad global exclusion count

From: Ambrish (ambrish.roy_at_gmail.com)
Date: Tue Oct 23 2007 - 01:45:05 CDT

Hi All

I am trying to equilibrate HIV protease with peptides. I have tried
configuration files similar to the examples used in Gramicin A and
Ubiquitin. However I have not been able to equilibrate the system. The error
is either

Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
Fatal error on PE 23 (it varies) > segmentation violation

 OR

Reason: FATAL ERROR: Bad global exclusion count!
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
Fatal error on PE 0 (it varies) > FATAL ERROR: Bad global exclusion count!

The errors does not occur at the same step, it varies. I have tried to
change the margin...box size but still the problem persists. I am using qsub
to submit it on my cluster.
I searched the mailing list but all the suggestions didn't work for me. I am
attaching my conf file as an attachment to this mail. Any help would be
greatly appreciated.

-- 
Best,
Ambrish Roy
Graduate Student
Dream is not that what you see in sleep...Dream is the thing which does not
allow you to sleep.
-- Dr. Abdul Kalam

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