[gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file

Sajjad Kavyani kavyani.sajjad at gmail.com
Sun Nov 29 16:20:32 CET 2015 

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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>>
>>
> --
> ==================================================
>
> 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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