[gmx-users] Broken trr-file

[Mark Abraham]

Hansjoerg Jerabek wrote:
> Dear colleagues!
> 
> I faced a problem while trying to modify a trr-file using trjconv_d:
> 
>     trjconv_d -f ketamine.t2.trr -s ketamine.2.tpr -n bilayer.ndx -o 
> ketamine.2.trr -b 43550
> 
> In my case the first frame of the trr-file starts at 43500ps (time step: 
> 5ps).
> I get the following ouput:
> 
>    Will write trr: Trajectory in portable xdr format
>    Reading file ketamine.2.tpr, VERSION 4.0.3 (double precision)
>    Reading file ketamine.2.tpr, VERSION 4.0.3 (double precision)
>    Select group for output
>    Group     0 (      System) has 25400 elements
>    Group     1 (        POPC) has 10400 elements
>    Group     2 (         SOL) has 15000 elements
>    Select a group: 0
>    Selected 0: 'System'
>    trn version: GMX_trn_file (double precision)
>    *Skipping frame      4 time 43520.000 *    
> -------------------------------------------------------
>    Program trjconv_d, VERSION 4.0.3
>    Source code file: trnio.c, line: 66
> 
>    *File input/output error:
>    Can not determine precision of trn file*
>    -------------------------------------------------------
> 
> It seems that the 4th frame at 43520ps is broken, but I somehow can't 
> get rid of it.

Assuming your file system isn't full or some such, the most likely 
problem is that the file was garbled when it was written. Check the log 
file for correct completion, and see what gmxcheck and/or gmxdump have 
to say about the .trr file. If the file's not been written correctly, 
there's nothing to do but re-run.

Mark