[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:
> 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
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
More information about the gromacs.org_gmx-users