Errors during equilibration: segmentation fault and bad global exclusion count

From: Ambrish (
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


Reason: FATAL ERROR: Bad global exclusion count!
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 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.

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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