[gmx-users] g_dist

Xavier Periole x.periole at rug.nl
Mon May 22 18:02:30 CEST 2006

Kay Gottschalk wrote:

> Hi there,
> we are doing a pulling simulation and want to monitor the distance  
> between two atoms during pulling. Using g_dist the distance is  
> calculated between all mirror images of the periodic boundary  
> conditions, and the minimal distance is calculated. In our case, this  
> is uncomfortable, since the distance should be monotonically  
> increasing, but since after approximately half of the simulation one  
> atoms starts to become closer to the mirror image in the next box, it  
> looks as if the distance is decreasing. Is it possible to switch off  
> the pbc condition in g_dist? I didn't find it in the manual or the  
> user list.

Is it any good to have your two atoms interacting through the images ??
It does not sound too good to me ...

You can just plot the distance and the size of the box (g_energy give 
the box size) and
then just substract the corresponding dimension if the box to the 
distance you
obtained with g_dist. I guess your are pulling on one of the axes !!!


 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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