From: Dongsheng Zhang <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@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.
Berk.
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