[gmx-users] how to skip corrupt frames in trr-file?

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 17 13:02:13 CET 2006

Alexandra Patriksson wrote:
> Hej,
> I have a trajectory file with an incomplete frame in the beginning. I am 
> only interested in the final ns of the trajectory but can not do any of 
> the analyses that I want to do just because of this corrupt frame in the 
> beginning - the programs stops. Neither can I make a new trajectory of 
> the final ns using trjconv, because trjconv also stops at the broken 
> frame. Is there any way for me  to get around this? I have also tried 
> the linux command split but it didn't give me any useful data.
> Thanks in advance
> Alexandra
Actually you didn't say it was a trr file. However, if you know the size 
of the frames you could use split to split off the last ns. Say your 
file = 10000 bytes and a single frame = 332 bytes, then you could get 
the last frame by starting at 10000 - 332 bytes using split. The only 
catch is that frames may be different size because not all have 
velocities (but the last one does).

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://folding.bmc.uu.se

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