[gmx-users] Corrupt TRR file -- skipping a bad frame?

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 27 01:10:51 CEST 2008

Matt Wyczalkowski wrote:
> I have a corrupt TRR file with a bad frame in the middle; I am
> wondering if I can remove just the bad frame to utilize all of my good
> data.
> To obtain the corrupt TRR file, I first ran a simulation which died
> (at about 37.9ns) due to a disk quota restriction; this first
> simulation produced part1.trr.  I restarted this simulation, and
> obtained part2.trr after the simulation finished successfully.  I then
> used trjcat to concatenate these simulations (not aware that part1.trr
> ended on a corrupt frame), and the data were appended to part1.trr.
> Finally, to save disk space, I deleted part2.trr, confident that all
> 60ns of simulation data were in part1.trr.

Lesson learned in being careful :)

> Not surprisingly, when I run any sort of analysis tool (including
> gmxcheck) it quits when it gets to the corrupt frame.  Ideally, I
> would like to remove just the offending frame.  I can use trjconv to
> extract the data up to the bad frame, but I can't use that utility to
> extract the good data past the bad frame, since it dies at the bad
> frame.

Unfortunately, even to extract frames, that bad frame has to be read, which will 
cause everything to crash.

The best bet is just to do it again.  Extract the viable data from the first 
part of the simulation and pick up from that point.  Then concatenate, check 
your output :), and proceed.


> For what its worth, part1.trr from the original run was about 2.1Gb,
> and part1 + part2 are about 3.4Gb.
> Any ideas how I could recover good data in a TRR file past a bad frame?
> Regards,
> Matt Wyczalkowski
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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