[gmx-users] centering molecule in the water box

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Tue Jul 1 12:12:31 CEST 2008

On Tuesday 01 July 2008 10:17, Fabio Affinito wrote:

if you have only one molecule in the box, and you are equilibrated, why would 
your molecule move around?
A visualization problem? Can you center it with editconf maybe?


> 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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Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de

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