Hi Amit,<br><br>My system is quite large, comprising of a molecule, water, and Na+ ions, summing up to 233863 (!) entities total. Regarding the segmentation fault, the MD simulation only ran for 2 steps before the system crashed.<br>
<br>Could the size of my system caused it to crash? Also, in my md.log file, the only error that I see is:<br><br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 10<br>
<br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br><br>Steepest Descents converged to machine precision in 36 steps,<br>
but did not reach the requested Fmax < 10.<br>Potential Energy = -6.9601880e+06<br>Maximum force = 4.1059329e+02 on atom 454<br>Norm of force = 2.6538130e+03<br><br><br>While I have encountered these messages before with other systems in the past, I did not encounter any major problems (i.e. segmentation faults) during their MD simulations.<br>
<br>Bests,<br>Lily<br><br><div class="gmail_quote">2009/11/13 Amit Choubey <span dir="ltr"><<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</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;">
hi,<div><br></div><div>could you specify the system size? </div><div><br></div><div>How many steps did it run before you got the segmentation fault? Try to find if everything went ok until the segmentation fault by saving log and trajectories.</div>
<div><br></div><font color="#888888"><div>amit</div></font><div><div></div><div class="h5"><div><br></div><div><br><br><div class="gmail_quote">On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><br>
<br>
<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,<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>
</blockquote>
<br></div>
Because mdrun is exiting, so the script is moving on. Perhaps the system isn't recognizing the $TPBCONV environment variable, and thus is interpreting "-s" as a separately command rather than an option passed to tpbconv.<br>
<font color="#888888">
<br>
-Justin</font><div><br>
<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<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>
<br>
========================================<br>
-- <br></div><div><div></div><div>
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></div>
</div></div><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">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<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">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></blockquote></div><br><br clear="all"><br>