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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