[gmx-users] trn file

[Justin A. Lemkul]

Maurício Menegatti Rigo wrote:
> With gmxcheck, I have the following:
> 
> 
> *Checking file File1.trr*
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time   10.000  
> # Atoms  47639
> Last frame         12 time   14.800  
> 
> 
> Item        #frames Timestep (ps)
> Step            13    0.4
> Time            13    0.4
> Lambda          13    0.4
> Coords          13    0.4
> Velocities      13    0.4
> Forces           0
> Box             13    0.4
> 
> *Checking file File2.trr*
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time   15.000  
> # Atoms  47639
> Last frame         12 time   19.800  
> 
> 
> Item        #frames Timestep (ps)
> Step            13    0.4
> Time            13    0.4
> Lambda          13    0.4
> Coords          13    0.4
> Velocities      13    0.4
> Forces           0
> Box             13    0.4
> 
> *Checking file File3.trr*
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time   20.000  
> # Atoms  47639
> Last frame         12 time   24.800  
> 
> 
> Item        #frames Timestep (ps)
> Step            13    0.4
> Time            13    0.4
> Lambda          13    0.4
> Coords          13    0.4
> Velocities      13    0.4
> Forces           0
> Box             13    0.4
> 
> *Checking file File4.trr*
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time   25.000  
> # Atoms  47639
> Last frame         12 time   29.800  
> 
> 
> Item        #frames Timestep (ps)
> Step            13    0.4
> Time            13    0.4
> Lambda          13    0.4
> Coords          13    0.4
> Velocities      13    0.4
> Forces           0
> Box             13    0.4
> 
> *Checking file File5.trr*
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time   30.000  
> # Atoms  47639
> Reading frame      70 time   58.000  
> -------------------------------------------------------
> Program gmxcheck, VERSION 4.0.7
> Source code file: trnio.c, line: 66
> 
> File input/output error:
> Can not determine precision of trn file
> -------------------------------------------------------
> 
> This means that my FIle5.trr stopped at time 58.0000 (the correct would 
> be 2000.0000)? IS THere any way to fix it?
> 
> Thanks !

Not likely.  If a frame is corrupt, tools like trjconv that can parse them out 
generally fail as well.  You can, however, use trjconv -e 58 to save the first 
frames of "File5.trr" and then continue on from a checkpoint to re-collect the 
remaining data.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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