[gmx-developers] Inconsistent shifts. trjconv bug?

[Erik Marklund]

16 apr 2012 kl. 11.32 skrev Erik Marklund:

> 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.


I gess my qustion is: should I file a redmine?

> 
> -----------------------------------------------
> 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
> 
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-----------------------------------------------
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

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