[gmx-users] Fwd: Segmentation fault while running gromacs 4.0.4

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 2 09:30:32 CEST 2009

Ms. Aswathy S wrote:
> Dept. Biotechnology
> Ext. 3108
> ----- Forwarded Message -----
> From: "Ms. Aswathy S" <aswathys at amritapuri.amrita.edu>
> To: gmx-users at gromacs.org
> 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 


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