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

Justin Lemkul jalemkul at vt.edu
Sun Nov 29 15:38:12 CET 2015 


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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