Ms. Aswathy S wrote:
Dept. Biotechnology
Ext. 3108
----- Forwarded Message -----
From: "Ms. Aswathy S" <[email protected]>
To: [email protected]
Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: Segmentation fault while running gromacs 4.0.4
Hi,
I am working in GROMACS 4.0.4 and trying to do a receptor -ligand simulation.
But when I run the grommp for equilibration of about 30 ps, it shows
Segmentaion Fault. I din't get any idea that what type of error it causing from
the log file. When i run the free command it has a free space of 33 MB. Is that
could be the reason?. But I already read that gromacs doesnot consume that much
memory(10-20Mb). If so tell me what could be the possibilities. attaching the
mdp file and log file
I will explain all the steps i have did,
1. The protein and ligand i minimized in vaccum.
2. Then added water and again minimized the whole system (During both 1 & 2 minimization,
"Steepest Descents converged to machine precision "in early steps )
3. I used the otput file from the above result for equilibration steps(is that
the reason??!!!)
then i faced the segmentatuion fault. Please help me....
Your simulation is blowing up
http://wiki.gromacs.org/index.php/blowing_up, probably because your
starting structure is badly broken (huge energy components, infinite
temperature).
Mark
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