[gmx-users] Broken trr-file

[Justin A. Lemkul]

Hansjoerg Jerabek wrote:
> 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.
> 

trjconv	-b 0 -e 3

You will have to sacrifice everything after frame 3 then (since frame 4 is 
corrupted).  Judging by the timeframe of the simulation, that is probably a 
substantial amount of data.  Perhaps you can restart from a checkpoint file, 
depending on how often those were written, to collect the rest of your data.

-Justin

> 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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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