[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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