<div>Hi Justin,</div>
<div> </div>
<div>Thanks for replying.</div>
<div> </div>
<div>No .log file is produced. Can you elaborate what do you mean by ' this really sounds more like a job for your sysadmin '. What should I exactly do to rectify this error? I am new to super computers and gromacs.</div>
<div> </div>
<div>Regards</div>
<div> </div>
<div>Shivkumar <br><br></div>
<div class="gmail_quote">On Thu, Dec 10, 2009 at 6:59 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>shivkumar bale wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Justin,<br> Sorry about the email. I just made a mistake while posting.<br> First of all, Thanks for replying.<br>
I tried the suggestions you gave like I changed the pbc from full to xyz, removed -Dflex term and also changed the fourier grid spacing but still I am getting the same error. I am attaching the error message with this email. Have a look at it. If you need any more information let me know.<br>
<br></blockquote><br></div>Have a look at the .log file produced by mdrun, if there is one. Otherwise, this really sounds more like a job for your sysadmin, since there is no Gromacs-related output that you have shown thus far to indicate that this is a Gromacs problem.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">Thanks for your help.<br> Regards<br> Shivkumar<br><br><br></div>
<div>
<div></div>
<div class="h5">On Tue, Dec 8, 2009 at 5:53 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br> You haven't addressed any of the comments or questions I posted earlier:<br><br> <a href="http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html</a><br>
<br> When asking for free help, demonstrate that you're willing to take<br> the advice you're given, and if that fails, state what problems<br> remain. Otherwise, it seems like you're ignoring viable suggestions.<br>
<br> For the sake of being explicit: your .mdp file is wrong, and the<br> dynamics are likely spurious. Solve these issues (which I have<br> described for you!) before moving to a more peripherally-related<br> solution. Also check the .log file; as I said before, Gromacs<br>
rarely exits without offering its own error messages about what's<br> going wrong. There is nothing in this output that immediately<br> suggests your PME spacing is remotely at fault, but other parameters<br> in your .mdp file are clearly wrong.<br>
<br> -Justin<br><br> shivkumar bale wrote:<br><br> Hi Gromacs Users,<br><br> The error:<br><br> mpispawn.c:303 Unexpected exit status<br><br> Child exited abnormally!<br> Killing remote processes...DONE<br>
<br> Following is the link which might help:<br><br> <a href="http://www.ece.unm.edu/~etanner/MPI.html" target="_blank">http://www.ece.unm.edu/~etanner/MPI.html</a><br> <<a href="http://www.ece.unm.edu/~etanner/MPI.html" target="_blank">http://www.ece.unm.edu/%7Eetanner/MPI.html</a><br>
<<a href="http://www.ece.unm.edu/~etanner/MPI.html" target="_blank">http://www.ece.unm.edu/~etanner/MPI.html</a>>><br><br><br><br></div></div>
<div class="im"> I think the above error is because of the PME calculations and<br> changing the grid spacing might work. But I dont know how to<br> change the grid spacing. Do you have any idea regarding that? Or<br>
if you think the error is due to some other reason let me know.<br><br> I am attaching the .mdp file with this email.<br><br> Thanks for the help.<br><br> Regards<br><br> Shivkumar<br><br><br>
-- ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> MILES-IGERT Trainee<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br>
</div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080
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<div class="h5"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<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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