[gmx-users] Energy file ener.edr not recognized, maybe different CPU?

[Justin Lemkul]

On 8/18/14, 8:15 AM, Kester Wong wrote:
> Hi Justin,
>
>
> THanks for the quick reply. I am concerned that it might be the ener.edr file
> that is fragmented, as the md.log report seem fine.
>
> Also, the same problem persisted even when the input files were migrated to a
> new folder for an energy minimisation calculation.
>
> For the second energy minimisation calculation, I even re-generated the
> system.ndx and topol.tpr files.
>

Are sensible energies reported in the corresponding .log file?  A run may 
"finish" but yield infinite energies if something failed.  That can also lead to 
an incorrect interpretation of .edr contents.  Again, running gmxcheck on all 
output files can be useful here.

-Justin

>
>
> Regards,
>
> Kester
>
>
>
> --------- 원본 메일 ---------
>
>     *보낸사람* : Justin Lemkul <jalemkul at vt.edu>
>     *받는사람* : <gmx-users at gromacs.org>
>     *받은날짜* : 2014년 8월 18일(월) 20:56:56
>     *제목* : Re: [gmx-users] Energy file ener.edr not recognized, maybe
>     different CPU?
>
>     On 8/18/14, 7:43 AM, Kester Wong wrote:
>     > Dear all,
>     >
>     >
>     > After the energy minimisation calculation, I plotted the (energy vs time)
>     > profile for some structures with the ener.xvg file.
>     >
>     >
>     > However, of all the energy minimised structures I have, one did not work.
>     >
>     > I have been trying to convert the energy minimised file "ener.edr" to "ener.xvg"
>     > using the command: g_energy_mpi -f ener.edr -o ener.xvg
>     >
>     >
>     > As the same procedure worked for all my other structures, this fatal error read:
>     >
>     > Program g_energy_mpi, VERSION 5.0
>     >
>     > Source code file: /home/choimin/Gromacs/gromacs-5.0/src/gromacs/fileio/enxio.c,
>     > line: 822
>     >
>     >
>     > Fatal error:
>     >
>     > Energy file ener.edr not recognized, maybe different CPU?
>     >
>     >
>     >
>     > The xvg file was successfully produced for other structures, why did it fail on
>     > this particular system?
>     >
>
>     Investigate the .log file and run gmxcheck on all of the output files of the
>     problematic run.  Likely it failed and produced fragmented output.
>
>     -Justin
>
>     --
>     ==================================================
>
>     Justin A. Lemkul, Ph.D.
>     Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>     Department of Pharmaceutical Sciences
>     School of Pharmacy
>     Health Sciences Facility II, Room 601
>     University of Maryland, Baltimore
>     20 Penn St.
>     Baltimore, MD 21201
>
>     jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>     http://mackerell.umaryland.edu/~jalemkul
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================