[gmx-developers] Inconsistent shifts. trjconv bug?

[Alexey Shvetsov]

Hi all!

I have similar problem with gromacs 4.5.5 and trajectories with ~10-20 
peptides

Erik Marklund писал 2012-04-16 12:32:
> Hi,
>
> I have a few trajectories from simulations of solvated proteins and
> DNA that causes problems when I pass them through trjconv. Here's the
> command line:
>
> trjconv  -f run.xtc -s run.tpr -o tst.xtc -pbc mol
>
> Choosing group "Protein" for output, I get heaps of inconsistent 
> shits:
>
> "...
> There were 1 inconsistent shifts. Check your topology00 time 4000.000
> There were 1 inconsistent shifts. Check your topology
> ..."
>
> These trajectories were saved frequently, some every 10 ps. If I use
> -dt 1000 the errors disappear, probably because I skip certain
> problematic frames. No problems were reported in the logfiles from 
> the
> simulations and this problem appears in braches release-4-6 and
> release-4-5-patches, and the official 4.5.5 release. The simulations
> were all done with release-4-5-patches.
>
> To me this looks like a bug.
>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru