[gmx-users] segmentation fault, very high KE but no high velocity

Dongsheng Zhang dong at pampas.chem.purdue.edu
Thu Jul 20 14:51:43 CEST 2006

Dear Berk,

Thank you for your reply. The velocities are from trr file. Could you
please tell me what those values are (for t-dt/2 or t+dt/2 or t)? If
they are not for time step t, could you change the source code to output
the value for t to keep consistency with KE? By the way, I had set 
nstfout  = 1, but I can't find the information for force in trr file. 

segmentation fault usually means that one array is out of bound. I set
cutoff as 1.4, the table extension as 2.0. My table covers the
interaction arrange of 5.0. I thought it should large enough. Just now I
extend my table to 10, I still get segmentation fault at the same time
step. Therefore I guess there is another reason to cause segmentation
fault. Could you please give me some suggestions? With your experiences,
could you please give me some general ideas what are possible causes for
segmentation fault?

All the best!


On Thu, 2006-07-20 at 09:20 +0200, Berk Hess wrote:
> >From: Dongsheng Zhang <dong at pampas.chem.purdue.edu>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: [gmx-users] segmentation fault, very high KE but no high velocity
> >Date: Wed, 19 Jul 2006 12:53:00 -0400
> >
> >Hello, gmx users,
> >
> >I got segmentation fault during a simulation. I outputted log, xtc, trr
> >file every step. From the log file, I can see that the KE is very high
> >in the last step, so I checked the velocities of particles in the last
> >step. Surprisingly there is no particle whose absolute value of the
> >velocity is over 100.  My question is where the very high KE from if the
> >velocities are not high. Could someone give me a sugestion about it and
> >how to figure out why I have segmentation fault. Thank you in advance!
> You have probably checked the velocities at t-dt/2,
> but KE is the average of t-dt/2 and t+dt/2.
> So you probably have particles coming to close
> or so far that an interaction tables in indexed out of range.
> Berk.
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