[gmx-users] Re: centering molecule in the water box

servaas michielssens servaas.michielssens at student.kuleuven.be
Tue Jul 1 12:20:50 CEST 2008

What box type are you using? Try adding following options

-center -pbc mol -ur compact

kind regards,


> 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  
> suggestion.
> Fabio

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