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

[Justin A. Lemkul]

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.:

http://wiki.gromacs.org/index.php/Membrane_Simulations#Adding_waters_with_genbox

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

-Justin

> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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