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
                  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/>
        <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/> <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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--
========================================

Justin A. Lemkul
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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