[gmx-users] Gmx_solvate

[rose rahmani]

Hi,

I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to
12 is empty) .  I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to start
from z=0 of box.
I mean when i extract wall and sheet from my last simulation and open it in
a viewer they wont start from 0, which is not odd. So i cant use the box
size 0 to 5(8-3) in z dimension, use gmx_solvate and then make the box
larger.
What is your idea? Is there any tool to add solvate in specific dimensions?
Would you please help me?

Best regards