[gmx-users] Broken trr-file

[Mark Abraham]

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