[gmx-users] Inconsistent shift warning in g_traj

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 7 15:09:34 CET 2006

Janne Hirvi wrote:
> Hello!
> I have tried to figure out method for calculation of the friction coefficient
> between graphite surfaces. I have simulated two infinite graphite surfaces with
> option pbc=full and everything seemed to be working properly. However, when I
> tried to extract coordinates, velocities, and forces of the center of mass of
> the graphite plane with g_traj (using option -com) I got numerous warnings
> about the inconsistent shifts: 
> I think that my topology-file for infinite graphite surface is correct and I
> would like to know what does this "warning" really mean and can I trust the
> results from g_traj anyway?
This is because g_traj does PBC anyway in the old way. For velocities 
and forces this shouldn't matter. For coordinates it could, but this is 
periodic anyway, so it may not be very informative.

> Thanks for any help or comments! 
> Janne
> ------------------------------------------------------------------------------
> Janne Hirvi, MSc(Physical Chemistry), Researcher
> University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
> Tel: +358 13 2514544 & +358 50 3474223
> E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
> ------------------------------------------------------------------------------
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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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