[gmx-users] Inconsistent shift warning in g_traj

[Xavier Periole]

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: 
>
>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?
>  
>
You might have different number of atoms in the traj file and in the 
file you use
for the topology !

XAvier

-- 
----------------------------------
 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole
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