[gmx-users] membrane protein tutorial

[leila karami]

Dear JustinI am using your tutorial (membrane protein) for my system.I
inserted my peptid into lipid bilayer. Now I want to solvate withwater using
genbox tool.To remove those water molecules are into lipid bilayer, I want
to usekeepbyz.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 moleculeHow to select upperz and lowerz? Based on
what criterion?If I want to have z vector = 9 nm after solvation, which
value ofupperz and lowerz are appropriate?If I use another way, only
reduction of the value of C from0.15 to 0.375 in vdwradii.dat file is
enough?Best wishes.

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