[gmx-users] unreadable frame in .trr file -help

David van der Spoel spoel at xray.bmc.uu.se
Sun Aug 8 16:39:58 CEST 2004

On Sun, 8 Aug 2004, Hadas Lapid wrote:

>Hi all,
>I ran a 10 ns trajectory, apparently at one point there was not enough 
>disk space, and the program wrote an unreadable  frame, never the less 
>the run did not crash, and when finished I could not view || analyze 
>the traj. beyond that point.
>Furthermore, when trying all options of trjconv to view the problematic 
>frame, extract it , skip it etc. the program could not continue  beyond 
>that point.
>Is there any way to "save" the rest of the trajectory?
You can use trjconv o split off the first part of the simulation (using 
the -e flag). Then you can determine the size in bytes of the frames and 
use a unix tool like split to break up the trr file, drop the corrupt 
part, and concatenate the rest to the a new trr file.

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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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