[gmx-users] membrane protein tutorial

[leila karami]

Dear Justin

I am using your tutorial (membrane protein) for my system.

I inserted my peptid into lipid bilayer. Now I want to solvate with
water using genbox tool.
To remove those water molecules are into lipid bilayer, I want to use
keepbyz.pl script by Chris Neale. In step 4 of this script:

4. use vi to edit keepbyz.pl
   - upperz and lowerz variables as you please
   - sol to the name of your solvent molecule

How to select upperz and lowerz? Based on what criterion?
If I want to have z vector = 9 nm after solvation, which value of
upperz and lowerz are appropriate?

If I use another way, only reduction of the value of C from
0.15 to 0.375 in vdwradii.dat file is enough?

Best wishes.