[gmx-users] Entending water in negative Z direction

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 4 22:17:23 CEST 2009


What is the difference between increasing in the positive z direction
and the negative z direction?


On Thu, Jun 4, 2009 at 4:31 PM, Anirban Ghosh <anirbanz83 at yahoo.co.in> wrote:
> Hi ALL,
> In previous posts I mentioned the problem I am facing: a portion of my
> protein (GPCR in a POPC bilayer) in extending out of the water box in
> negative Z-direction, how to extend the water in that direction. I have gone
> through the PBC section of the manual. While changing the Z coordinate value
> of the last line of the .gro file I am able to extend the water layer in the
> positive Z direction. But I am not able to extend it in the opposite
> direction. Decreasing the Z coordinate value is not helping that. How to do
> this? Any suggestion is welcome.
> Regards,
> Anirban Ghosh
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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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