[gmx-users] Re: Extend water layer along negative Z-direction

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jun 1 09:06:31 CEST 2009

Hi Anirban,

You have to get a grip on PBC. What you're suggesting is like
extending the earth only westward, but not eastward as something is
sticking out in only one direction. It's impossible! The system is
periodic.The box vectors are direction vectors, indicating the
periodicity. Moreover, you're command to extend the box (-box 0 0
-3.5) tries to set a box with vector _lengths_ 0, 0 and -3.5. Maybe a
good idea to read Chapter 3 of the manual, regarding periodic boundary



On Mon, Jun 1, 2009 at 8:24 AM, Anirban Ghosh <anirbanz83 at yahoo.co.in> wrote:
> Hi ALL,
> Thanks a lot Chris, Justin and Tsjerk for yor replies.
> Actually, my problem is not fully resolved. A portion of the protein tail is
> outside the water box in the Z direction (coordinate in Z is -35). So as
> suggested by you when I am issuing the command "editconf -f box.gro -o
> BOX.gro -box 0 0 -3.5", but after that genbox is giving the error:
> Fatal error:
> Undefined solute box.
> Create one with editconf or give explicit -box command line option
> Please can you specify the proper command, so that the water box is extended
> only in the negative Z direction (to solvate the portion of the protein out
> of the box)
> Regards,
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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