[gmx-developers] Inconsistent shifts. trjconv bug?

Erik Marklund erikm at xray.bmc.uu.se
Mon Apr 16 11:32:03 CEST 2012


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

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