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

Dongsheng Zhang dong at pampas.chem.purdue.edu
Thu Jul 20 15:36:17 CEST 2006

On Thu, 2006-07-20 at 14:55 +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: RE: [gmx-users] segmentation fault, very high KE but no high 
> >velocity
> >Date: Thu, 20 Jul 2006 08:51:43 -0400
> >
> >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.
> >
> The velocities in the trr are at step t-dt/2.
> With the leap-frog integrator the velocities are never
> determined at time t (read the manual).
> >
> >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?
> The most probable cause in an instability in your system, which
> causes very high forces. If you are lucky you can see it in
> the configuration or the forces one integration step before the crash.

I don't know why I can't get the force information it trr even though I
set nstfout  = 1. When I check my successful simulation, I can get the
force information in trr file. Do you think segmentation fault can
affect that? (sounds weird) If some particle comes too close, the
potential should be very high. From the log file, it looks fine
(even for the last step). The following is from the log file:

           Step           Time         Lambda
           2888     6985.77588        0.00000

   Energies (kJ/mol)
           Bond          Angle          LJ-14     Coulomb-14        LJ
    1.15825e+04    2.30097e+04    1.63992e+02    7.07392e+01   -1.36352e
   Coulomb (SR)      Potential    Kinetic En.   Total Energy
    0.00000e+00   -1.01525e+05    2.85627e+12    2.85627e+12    2.89201e
 Pressure (bar)

Thank you for your help!

> Berk.
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