[gmx-users] Broken trr-file

[Hansjoerg Jerabek]

Mark Abraham wrote:
> Justin A. Lemkul wrote:
>>
>>
>> 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.
>
> ... and next time, plan to save yourself data suitable for a restart 
> every few compute hours or so!
>
> There's some general information here, but the detail was written for 
> GROMACS 3.3.x. http://wiki.gromacs.org/index.php/Doing_Restarts
>
> Mark

... thank you for your advices. since it was impossible to edit the 
trr-file with any of the gromacs application, I used a hex-editor and a 
small c++-application to cut the broken frames out.

best regards
hansjoerg