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

[chris.neale at utoronto.ca]

Hi Anirban,

The first thing that you need to do is to use editconf to increase  
your box z and then genbox to add more solvent. My script (and  
C-program) do not do this, they focus only on removing waters that are  
placed within your bilayer.

Check out the wiki information.
http://wiki.gromacs.org/index.php/Membrane_Simulations

Chris.

-- original message --

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.

Regards,

Anirban Ghosh