[gmx-users] centering molecule in the water box

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 1 12:30:43 CEST 2008

Fabio Affinito wrote:
> 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.

When prompted for a group to center, what are you choosing?  It sounds 
like you've chosen 'System' if everything is moving.  Try centering with 
respect to your molecule of interest.


> I also checked the gmx-users list and I didn't get any useful suggestion.
> Fabio
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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