[gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file
Sajjad Kavyani
kavyani.sajjad at gmail.com
Sun Nov 29 23:53:04 CET 2015
Dear Teemu,
I visited the webpage and as you said it was certainly related.
I could manage the problem by switching to a 64-bit OS (UBUNTU) and it
seems that the problem is gone.
Thank you all for the help
Sajjad
On Sun, Nov 29, 2015 at 7:30 PM, Teemu Murtola <teemu.murtola at gmail.com>
wrote:
> http://redmine.gromacs.org/issues/1834 is possibly related. But there is
> not enough information in that issue to understand what exactly is wrong,
> or for providing an actual fix.
>
> Best regards,
> Teemu
>
> On Sun, Nov 29, 2015, 17:20 Sajjad Kavyani <kavyani.sajjad at gmail.com>
> wrote:
>
> > Hi,
> > Thanks so much for the response.
> > The resulted files were copied from an external NTFS HD to the ext4 file
> > system (UBUNTU installation partition). Reading from both terminates the
> > analysis.
> > I can read and analyse the NVT, NPT or em.trr files (other .trr or .xtc
> > files), but as you mentioned the problem might be with >2GB condition.
> > And it is noteworthy that the VMD can easily open and read them (the
> md.trr
> > files)!!
> >
> > So where is the problem? Could you please help me to find and solve that?
> >
> > -Sajjad
> >
> > On Sun, Nov 29, 2015 at 6:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 11/29/15 9:28 AM, Erik Marklund wrote:
> > >
> > >> Dear Sajjad,
> > >>
> > >> As you can see, you don’t have a file called md.trr. Provide another
> > file
> > >> with the -f option.
> > >>
> > >>
> > > It's there, along with md.xtc, but both are > 2 GB, so the file system
> > > probably cannot handle files of that size given that neither can be
> > opened.
> > >
> > > -Justin
> > >
> > >
> > > Kind regards,
> > >> Erik
> > >>
> > >> On 29 Nov 2015, at 11:45, Sajjad Kavyani <kavyani.sajjad at gmail.com>
> > >>> wrote:
> > >>>
> > >>> Dear all,
> > >>> Recently, I simulated a system with gromacs 5.0.4. But now, when I am
> > >>> trying to run a g_gyrate (or any other) a fatal error appear with:
> > >>>
> > >>> Can not open file:
> > >>> md.trr
> > >>> For more information and tips for troubleshooting, please check the
> > >>> GROMACS
> > >>> website...
> > >>>
> > >>> This is also happened with the .xtc file.
> > >>>
> > >>> The ls -l output :
> > >>>
> > >>> -rw-r--r-- 1 sajjad sajjad 780 Aug 2 11:03 em.edr
> > >>> -rw-r--r-- 1 sajjad sajjad 412160 Aug 2 11:03 em.gro
> > >>> -rw-r--r-- 1 sajjad sajjad 15619 Aug 2 11:03 em.log
> > >>> -rw-r--r-- 1 sajjad sajjad 3103 Aug 2 11:03 em.mdp
> > >>> -rw-r--r-- 1 sajjad sajjad 3104 Aug 2 11:03 em.mdp~
> > >>> -rw-r--r-- 1 sajjad sajjad 262120 Aug 2 11:03 em.tpr
> > >>> -rw-r--r-- 1 sajjad sajjad 110016 Aug 2 11:03 em.trr
> > >>> -rw-r--r-- 1 sajjad sajjad 17105 Aug 2 11:03 G5_box.gro
> > >>> -rw-r--r-- 1 sajjad sajjad 104065 Aug 2 11:03 G5_copy.itp
> > >>> -rw-r--r-- 1 sajjad sajjad 17105 Aug 2 11:03 G5.gro
> > >>> -rw-r--r-- 1 sajjad sajjad 104065 Aug 2 11:07 G5.itp
> > >>> -rw-r--r-- 1 sajjad sajjad 104065 Aug 2 11:03 G5.itp~
> > >>> -rw-r--r-- 1 sajjad sajjad 636064 Aug 2 11:07 G5.ods
> > >>> -rw-r--r-- 1 sajjad sajjad 412160 Aug 2 11:03 G5_water.gro
> > >>> -rw-r--r-- 1 sajjad sajjad 886305 Aug 2 11:03 gyrate2.xvg
> > >>> -rw-r--r-- 1 sajjad sajjad 653382 Aug 2 11:03 gyrate2.xvg~
> > >>> -rw-r--r-- 1 sajjad sajjad 141214 Aug 2 11:03 index.ndx
> > >>> -rw-r--r-- 1 sajjad sajjad 153 Aug 2 11:03 ion.itp
> > >>> -rw-r--r-- 1 sajjad sajjad 940 Aug 2 11:03 ions.mdp
> > >>> -rw-r--r-- 1 sajjad sajjad 50981 Aug 2 11:03 martini_v2.2.itp~
> > >>> -rw-r--r-- 1 sajjad sajjad 50994 Aug 2 11:03
> > >>> martini_v2.2_P1P5mod.itp
> > >>> -rw-r--r-- 1 sajjad sajjad 50917 Aug 2 11:03
> > >>> martini_v2.2_P1P5mod.itp~
> > >>> -rw-r--r-- 1 sajjad sajjad 221556 Aug 2 11:03 md.cpt
> > >>> -rw-r--r-- 1 sajjad sajjad 38727904 Aug 2 11:07 md.edr
> > >>> -rw-r--r-- 1 sajjad sajjad 631991 Aug 2 11:03 md_extract.gro
> > >>> -rw-r--r-- 1 sajjad sajjad 631952 Aug 2 11:03 md.gro
> > >>> -rw-r--r-- 1 sajjad sajjad 33962116 Aug 2 11:03 md.log
> > >>> -rw-r--r-- 1 sajjad sajjad 4021 Aug 2 11:03 md.mdp
> > >>> -rw-r--r-- 1 sajjad sajjad 4021 Aug 2 11:07 md.mdp~
> > >>> -rw-r--r-- 1 sajjad sajjad 11575 Aug 2 11:03 mdout.mdp
> > >>> -rw-r--r-- 1 sajjad sajjad 221556 Aug 2 11:03 md_prev.cpt
> > >>> -rw-r--r-- 1 sajjad sajjad 262036 Aug 2 11:03 md.tpr
> > >>> -rw-r--r-- 1 sajjad sajjad 3301099032 Aug 2 11:07 md.trr
> > >>> -rw-r--r-- 1 sajjad sajjad 3540368244 Aug 2 11:07 md.xtc
> > >>> -rw-r--r-- 1 sajjad sajjad 221556 Aug 2 11:03 npt.cpt
> > >>> -rw-r--r-- 1 sajjad sajjad 414904 Aug 2 11:03 npt.edr
> > >>> -rw-r--r-- 1 sajjad sajjad 631952 Aug 2 11:03 npt.gro
> > >>> -rw-r--r-- 1 sajjad sajjad 379243 Aug 2 11:07 npt.log
> > >>> -rw-r--r-- 1 sajjad sajjad 4058 Aug 2 11:07 npt.mdp
> > >>> -rw-r--r-- 1 sajjad sajjad 4057 Aug 2 11:03 npt.mdp~
> > >>> -rw-r--r-- 1 sajjad sajjad 221556 Aug 2 11:03 npt_prev.cpt
> > >>> -rw-r--r-- 1 sajjad sajjad 262120 Aug 2 11:03 npt.tpr
> > >>> -rw-r--r-- 1 sajjad sajjad 35405832 Aug 2 11:03 npt.trr
> > >>> -rw-r--r-- 1 sajjad sajjad 37885780 Aug 2 11:03 npt.xtc
> > >>> -rw-r--r-- 1 sajjad sajjad 221300 Aug 2 11:03 nvt.cpt
> > >>> -rw-r--r-- 1 sajjad sajjad 44960 Aug 2 11:07 nvt.edr
> > >>> -rw-r--r-- 1 sajjad sajjad 631952 Aug 2 11:03 nvt.gro
> > >>> -rw-r--r-- 1 sajjad sajjad 63990 Aug 2 11:03 nvt.log
> > >>> -rw-r--r-- 1 sajjad sajjad 4053 Aug 2 11:03 nvt.mdp
> > >>> -rw-r--r-- 1 sajjad sajjad 4053 Aug 2 11:03 nvt.mdp~
> > >>> -rw-r--r-- 1 sajjad sajjad 221300 Aug 2 11:03 nvt_prev.cpt
> > >>> -rw-r--r-- 1 sajjad sajjad 262120 Aug 2 11:03 nvt.tpr
> > >>> -rw-r--r-- 1 sajjad sajjad 4618152 Aug 2 11:03 nvt.trr
> > >>> -rw-r--r-- 1 sajjad sajjad 4856648 Aug 2 11:07 nvt.xtc
> > >>> -rw-rw-r-- 1 sajjad sajjad 696 Nov 29 15:03 PI_G3rg.xvg
> > >>> -rw-r--r-- 1 sajjad sajjad 188 Aug 2 11:03 posre_com.itp
> > >>> -rw-r--r-- 1 sajjad sajjad 16412 Aug 2 11:03 posre.itp
> > >>> -rw-r--r-- 1 sajjad sajjad 15275 Aug 2 11:07 posre.itp~
> > >>> -rw-r--r-- 1 sajjad sajjad 229 Aug 2 11:03 topol.top
> > >>> -rw-r--r-- 1 sajjad sajjad 229 Aug 2 11:03 topol.top~
> > >>> -rw-r--r-- 1 sajjad sajjad 27643 Aug 2 11:03 water.gro
> > >>>
> > >>> I would be very grateful if you can help me.
> > >>>
> > >>> With regards
> > >>> Sajjad
> > >>> --
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> > >>>
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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 629
> > > 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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