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
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