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

[Erik Marklund]

Dear Sajjad,

As you can see, you don’t have a file called md.trr. Provide another file with the -f option.

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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