On 4/16/18 5:58 AM, rose rahmani wrote:
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?
Write a script to remove solvent molecules based on coordinates, or use gmx select write an index group to do the same.
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