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

[chris.neale at utoronto.ca]

The point of the script on
http://wiki.gromacs.org/index.php/Membrane_Simulations#Adding_waters_with_genbox
is not intended as a replacement for what Justin describes, which is  
always necessary. The point is that when you do this you will have  
lots of waters placed into your bilayer. While it is possible to  
simply equilibrate these out, one may speed up equilibration by simply  
removing any waters that go into the bilayer... and that is the  
purpose of keepbyz.sh (or keepbyz.c, which is certainly a better  
approach -- I probably should have removed keepbyz.sh from the wiki as  
it is much slower).

Chris.


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