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! Dongsheng On Thu, 2006-07-20 at 09:20 +0200, Berk Hess wrote: > > > >From: Dongsheng Zhang <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users <[email protected]> > >To: Discussion list for GROMACS users <[email protected]> > >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. > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
