[gmx-users] Broken trr-file

Hansjoerg Jerabek hansjoerg.jerabek at arcs.ac.at
Wed Mar 11 13:25:39 CET 2009


Dear Mark!

At first: thanks for your reply.

The log file has been witten correctly, and gmxcheck gives me the 
following warning:

    Checking file ketamine.t2.trr
    trn version: GMX_trn_file (double precision)
    Reading frame       0 time 43500.000  
    # Atoms  25400
    Reading frame       4 time 43520.000   Warning at frame 4: 
coordinates for atom 21839 are large (3.04738e+35)
    Warning at frame 4: coordinates for atom 21839 are large (2.16053e+185)

    -------------------------------------------------------
    Program gmxcheck_d, VERSION 4.0.3
    Source code file: trnio.c, line: 66

    File input/output error:
    Can not determine precision of trn file
    -------------------------------------------------------

Is it somehow possible to manually remove the corrupt frame from the 
binary trr-file?
I'm asking this because I can't afford to re-run the simulation, since 
it would take about 3 weeks.

Best regards
Hansjoerg Jerabek



Mark Abraham wrote:
> 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
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