Hi, I received a similar error during an equilibration by steepest descent in which I had posed constraints on water, leaving the protein free to move. I suggest to control your mdp file... maybe you did the same thing and the system collapsed or exploded (you can see that reading the log file: if this is the cause, you should see problems regarding water).
Cheers, Annalisa 2009/4/13 Justin A. Lemkul <[email protected]> > > > nam kim wrote: > >> process crashes around 100 steps out of 1000 requested. >> >> > Fine, but you still haven't answered my question. Do you receive any other > messages? > > Do other systems run on the specific hardware you're using? You may just > have some instability in this particular system that is causing a crash. > Examine the trajectory, see what's going wrong, and post any other > relevant error messages, if you receive any. Often times there is some > output before a seg fault. > > -Justin > > > On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul <[email protected]> >> wrote: >> >>> >>> nam kim wrote: >>> >>>> I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). >>>> I have installed gromacs 4.0.4 two month ago and been working fine. >>>> Today, I just got Segment errors. Rebooting does not much help. >>>> >>>> Here is log: >>>> >>>> [rd:06790] *** Process received signal *** >>>> [d:06790] Signal: Segmentation fault (11) >>>> [rd:06790] Signal code: (128) >>>> [rd:06790] Failing at address: (nil) >>>> [rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430] >>>> [rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496] >>>> [rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e] >>>> [rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a] >>>> [rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552] >>>> [rd:06790] [ 5] >>>> /usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0] >>>> [rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32] >>>> [rd:06790] *** End of error message *** >>>> >>>> Are there any other messages from mdrun? Anything printed to the >>> screen >>> (LINCS warnings, etc)? >>> >>> -Justin >>> >>> Thanks >>>> _______________________________________________ >>>> gmx-users mailing list [email protected] >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> 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 >>>> >>>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Graduate Research Assistant >>> ICTAS Doctoral Scholar >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> 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 >>> >>> >> > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 >
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