[gmx-users] Re: corrupt trajectory
spoel at xray.bmc.uu.se
Fri May 27 17:05:31 CEST 2005
On Fri, 2005-05-27 at 10:38 -0400, Amil Anderson wrote:
> Since I've successfully read over 12 GB of the file (~14.9% of the
> file), I don't think that a 2 GB file size limit is the problem.
> Also, trjconv stops at the same frame number in both the .trr and
> .xtc files which are different sizes.
Then your files may be corrupt due to e.g. file server problems. You may
want to check the archives for workarounds. In the near future we will
have a mechanism for random access to xtc files which in principle means
you should be able to hop over broken frames.
> >On Thu, 2005-05-26 at 19:47 -0400, Amil Anderson wrote:
> >> I have recently finished a very long MD simulation that created a 87
> >> Gigabyte .trr trajectory file and a 23 Gigabyte .xtc file. When
> >> using trjconv to sample these trajectories the programs fails on the
> >> 148,760th frame with a fatal error: "Can not determine precision of
> >> trn file". The fatal error occurs at the same frame when I am
> >> reading either the .trr or the .xtc file. Is there a way to get to
> >> the remaining 85% of the file?
> >> I have tried skipping the first 149,000 frames using the -b option
> >> but still get caught at frame 148,760
> >Does your OS have file size limitation at 2 Gb?
> >> Thanks for any assistance that can be provided.
> >> Amil Anderson
> >> Associate Professor of Chemistry
> >> Wittenberg University
> >> Springfield, OH 45501
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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