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

Justin A. Lemkul jalemkul at vt.edu
Sat May 30 13:14:20 CEST 2009

Anirban Ghosh wrote:
> Hi ALL,
> I have a system of a GPCR protein in a lipid bilayer. I want to extend
> the water layer along the negative Z-direction. I found a script by Chris
> at the GROMACS mail list. But I am unable to use it properly. Can anyone
> please explain how to use it to extend the water layer only in the
> negative Z-direction. And also what does "upeerz and lowerz" signify? Is 
> it for the protein or the water layers? Thanks a lot in advance.

If the script isn't working out for you, there is another approach.  Position 
your system within the appropriately-sized box with editconf (specifying the 
appropriate -center), then use genbox, i.e.:


If you have placed the membrane appropriately, genbox will fill the rest of the 
empty space with water.


> Regards,
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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