Hi,<br><br>The relevant lines of my script are the following:<br><br>line 27: # Run MD and write output to /nas2 disk<br>line 28: $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr<br>
line 29:<br>line 30: # MDRUN completes: now make the next run file for a further 200 ps, to be run by next job<br>line 31: $TPBCONV -s npg3_4.tpr -f npg3_4.trr -e npg3_4.edr -o npg3_4_2.tpr -extend 200000<br><br><br>Since line 31 would be carried out after line 28, I'm not sure why the comment "-s: command not found" is relevant?<br>
<br>Lily<br><br><div class="gmail_quote">2009/11/13 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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"><a href="mailto:rainy908@yahoo.com" target="_blank">rainy908@yahoo.com</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;">
Hi all,<br>
<br>
I've encountered a problem while trying to run Gromacs on my coarse-grained molecule. I've already performed the initial energy minimization. I tried to run the inital MD simulation, but the job was cut short due to a segmentation fault, as mentioned in the output file:<br>
<br>
^Mstep 0^Mstep 100, will finish Wed Dec 16 16:55:17 2009^Mstep 200, will finish Wed Dec 16 07:04:11 2009^Mstep 300, will finish Wed Dec 16 12:59:33 2009^Mstep 400, will finish Wed Dec 16 09:02:03 2009^Mstep 500, will finish Wed Dec 16 12:12:01 2009^Mstep 600, will finish Wed Dec 16 14:18:47 2009^Mstep 700, will finish Wed Dec 16 15:49:22 2009^Mstep 800, will finish Wed Dec 16 13:29:16 2009^Mstep 900, will finish Wed Dec 16 14:45:15 2009^Mstep 1000, will finish Wed Dec 16 15:46:03 2009<br>
<br>
/opt/gridengine/default/spool/<br>
compute-0-7/job_scripts/182710: line 28: 18851 Segmentation fault (core dumped) $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr<br>
/opt/gridengine/default/spool/compute-0-7/job_scripts/182710: line 31: -s: command not found<br>
</blockquote>
<br></div>
So what's on line 31 of your submission script? The above is just stderr and stdout, which are not the main output. What's in the .log file?<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>