[gmx-users] Inconsistent shift warning in g_traj

[Janne Hirvi]

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: 

THERE WERE 198 INCONSISTENT SHIFTS. CHECK YOUR TOPOLOGY.

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?


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
------------------------------------------------------------------------------