<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Hi Justin, </p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">I think I might have used a pretty small Fmax value for my system of 2000+ water molecules.</p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">The md.log file reports:</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Steepest Descents converged to machine precision in 14 steps,</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">but did not reach the requested Fmax < 200.</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Potential Energy = 7.9771407e+19</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Maximum force = inf on atom 33772</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Norm of force = inf</p><div style="font-family: Gulim; font-size: 10pt;"><br></div><div style="font-family: Gulim; font-size: 10pt;"><br></div><div style="font-family: Gulim; font-size: 10pt;">I guess this issue would be corrected using emtol = 1000?</div><div style="font-family: Gulim; font-size: 10pt;"><br></div><div style="font-family: Gulim; font-size: 10pt;">Regards,</div><div style="font-family: Gulim; font-size: 10pt;">Kester</div><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><div style="font-family: 돋움, arial; font-size: 12px; margin-top: 30px; margin-left: 0.8em; color: rgb(0, 102, 204); font-weight: bold;">--------- 원본 메일 ---------</div><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><b>보낸사람</b> : Justin Lemkul <jalemkul@vt.edu><br><b>받는사람</b> : <gmx-users@gromacs.org><br><b>받은날짜</b> : 2014년 8월 19일(화) 01:44:08<br><b>제목</b> : Re: [gmx-users] Energy file ener.edr not recognized, maybe different CPU?<br><!-- original content --><div style="margin-top:5px;"><pre>
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@vt.edu>
> *받는사람* : <gmx-users@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@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request@gromacs.org.
>
>
>
>
--
==================================================
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@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request@gromacs.org.
</gmx-users@gromacs.org></jalemkul@vt.edu></pre></div><!-- original content --><br></div></blockquote></p>
<img src='http://mail.ibs.re.kr/checkread/NjY0Njk0/Z214LXVzZXJzQGdyb21hY3Mub3Jn/' width='1px' height='1px' />