shivkumar bale wrote:
Hi Justin,
Now I am able to get the output but the error is still coming.
I am attaching .log file and error file with this email. This might help.
Thanks for helping all of us.
First, upgrade to the latest Gromacs version. It takes care of lots of little
bugs. Perhaps not directly related, but you should always use the newest
version, unless you have a compelling reason to use an old one (i.e.,
consistency with previous work).
Second, your potential energy is extremely high. You have probably not done
sufficient energy minimization, which is causing your system to collapse
immediately.
-Justin
Regards
Shivkumar
On Thu, Dec 10, 2009 at 7:31 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
shivkumar bale wrote:
Hi Justin,
Thanks for replying.
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.
If no output is produced, then there are plenty of potential
problems - faulty Gromacs installation, buggy MPI implementation
(they are out there!), node problems, etc. Whoever is in charge of
the cluster (your system administrator) may be able to probe system
log files or run debug analysis to see what's wrong. There's
nothing more anyone here can likely provide.
-Justin
Regards
Shivkumar
On Thu, Dec 10, 2009 at 6:59 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
shivkumar bale wrote:
Hi Justin,
Sorry about the email. I just made a mistake while posting.
First of all, Thanks for replying.
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.
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.
-Justin
Thanks for your help.
Regards
Shivkumar
On Tue, Dec 8, 2009 at 5:53 AM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:
You haven't addressed any of the comments or questions I
posted earlier:
http://lists.gromacs.org/pipermail/gmx-users/2009-December/047294.html
When asking for free help, demonstrate that you're
willing to
take
the advice you're given, and if that fails, state what
problems
remain. Otherwise, it seems like you're ignoring viable
suggestions.
For the sake of being explicit: your .mdp file is
wrong, and the
dynamics are likely spurious. Solve these issues
(which I have
described for you!) before moving to a more
peripherally-related
solution. Also check the .log file; as I said before,
Gromacs
rarely exits without offering its own error messages
about what's
going wrong. There is nothing in this output that
immediately
suggests your PME spacing is remotely at fault, but other
parameters
in your .mdp file are clearly wrong.
-Justin
shivkumar bale wrote:
Hi Gromacs Users,
The error:
mpispawn.c:303 Unexpected exit status
Child exited abnormally!
Killing remote processes...DONE
Following is the link which might help:
http://www.ece.unm.edu/~etanner/MPI.html
<http://www.ece.unm.edu/%7Eetanner/MPI.html
<http://www.ece.unm.edu/~etanner/MPI.html>
<http://www.ece.unm.edu/~etanner/MPI.html>
<http://www.ece.unm.edu/~etanner/MPI.html>>
I think the above error is because of the PME
calculations and
changing the grid spacing might work. But I dont
know how to
change the grid spacing. Do you have any idea
regarding
that? Or
if you think the error is due to some other reason
let me
know.
I am attaching the .mdp file with this email.
Thanks for the help.
Regards
Shivkumar
-- ========================================
Justin A. Lemkul
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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