[gmx-users] centering molecule in the water box

Fabio Affinito affinito at sissa.it
Tue Jul 1 10:17:07 CEST 2008

Hi all,
During my MD the molecule experience a drift. Now I want to put the  
molecule at the center of the water box.
I tried with trjconv using the -pbc mol and -center flag and using a  
reference frame where the molecule is at the center of the box.
It seems that all the box (water+molecule) is translated, and so the  
position of the molecule relatively to the box is unchanged.
I also checked the gmx-users list and I didn't get any useful  


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