VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Wed May 10 2006 - 04:22:34 CDT

Hi Tzu-Lan,

I do not see any way for doing it except wrapping all the water in the
simulation box. Actually, one should put the protein in the center
and then wrap all the water back.
There is a tcl-script, which does that at

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/

but I didn't try it up to now.

Hope, this will help.

Eddi

On Wednesday 10 May 2006 07:11, TZU-LAN YEH wrote:
> Dear VMD users,
>
> I want to monitor water around a certain residue, but my protein is
> drifting out of the water box. When I used the selection "water and
> within * of resid # ", VMD showed the water molecules within the
> distance, but only those inside the box. When I turn on peridoic
> cell in the diection protein drifting, VMD still wouldn't show
> those water molecules. Neither did they appear on the other side of
> the water box. Could someone give me some advises how to solve this
> problem?
>
> Thank you in advance.
>
> Tzu-Lan 

-- 
--
=======================================================================
Eduard Schreiner                        e-mail: 
eduard.schreiner_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)
234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)
234/32-14045
D-44780 Bochum                               
http://www.theochem.rub.de
=======================================================================