[gmx-users] g_dist

[Kay Gottschalk]

They are not interacting. The distance is larger than 40 Å. But  
still,if the distance to the mirror image is 41 Å and to the same  
protein in the box is 45 Å, the distance to the mirror image will be  
plotted... We are indeed pulling on z.
Best, Kay.

On May 22, 2006, at 6:02 PM, Xavier Periole wrote:

> 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
>
> -- 
> ----------------------------------
> 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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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kay-Eberhard Gottschalk
Applied Physics and Center for Nano Sciences
Ludwig-Maximilians University
Amalienstr. 54
80799 Munich, Germany

Phone: +49-89-2180 3436