Hi,<br>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.<br>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).<br>
<br>Cheers,<br>Annalisa<br><br><div class="gmail_quote">2009/4/13 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
nam kim wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
process crashes around 100 steps out of 1000 requested.<br>
<br>
</blockquote>
<br></div>
Fine, but you still haven't answered my question. Do you receive any other messages?<br>
<br>
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.<br>
<font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
nam kim wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4).<br>
I have installed gromacs 4.0.4 two month ago and been working fine.<br>
Today, I just got Segment errors. Rebooting does not much help.<br>
<br>
Here is log:<br>
<br>
[rd:06790] *** Process received signal ***<br>
[d:06790] Signal: Segmentation fault (11)<br>
[rd:06790] Signal code: (128)<br>
[rd:06790] Failing at address: (nil)<br>
[rd:06790] [ 0] /lib64/tls/libpthread.so.0 [0x36bc30c430]<br>
[rd:06790] [ 1] /lib64/ld-linux-x86-64.so.2 [0x36bb607496]<br>
[rd:06790] [ 2] /lib64/ld-linux-x86-64.so.2 [0x36bb60789e]<br>
[rd:06790] [ 3] /lib64/ld-linux-x86-64.so.2 [0x36bb60a68a]<br>
[rd:06790] [ 4] /lib64/ld-linux-x86-64.so.2 [0x36bb60a552]<br>
[rd:06790] [ 5]<br>
/usr/local/topspin/lib64/libvapi.so(vipul_cleanup+0x50) [0x2a984472b0]<br>
[rd:06790] [ 6] /usr/local/topspin/lib64/libvapi.so [0x2a98440c32]<br>
[rd:06790] *** End of error message ***<br>
<br>
</blockquote>
Are there any other messages from mdrun? Anything printed to the screen<br>
(LINCS warnings, etc)?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks<br>
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========================================<br>
<br>
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Virginia Tech<br>
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-- <br><div><div></div><div class="h5">
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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