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

[Alan Dodd]

I'm sure I have, in the past, found a way to use trjcat/trjconv to overwrite a bad frame with a good one.  From memory, I had to convert the area around the bad frame to pdb/gro (for some reason that worked where normal tools didn't), open up the files, rewrite several bad frames (just copied and pasted good frames onto it), and then converted it back to trr/xtc.  It may have only worked due to being a special case, but it might be worth looking for that in the archives - I remember mentioning it before.
I'd love to know what the rules are for which file trjcat takes frames from, when there's an option, actually...



----- Original Message ----
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: jalemkul at vt.edu; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, August 27, 2008 9:21:10 AM
Subject: Re: [gmx-users] Corrupt TRR file -- skipping a bad frame?

Hi Matt,

You can determine the size of a single frame in bytes from what you
have and use 'split' to split up your corrupt trajectory. Now the
corrupt frame may not have the correct size, so you'll probably have
to think of a way to start splitting from the end.

Cheers,

Tsjerk

On Wed, Aug 27, 2008 at 1:10 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>
> -Justin
>
>>
>> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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