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

[David van der Spoel]

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.
________________________________________________________________________
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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