[gmx-users] Entending water in negative Z direction

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 4 21:33:12 CEST 2009

Anirban Ghosh 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.
Increase the z-coordinate.

> Regards,
> *Anirban Ghosh*
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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