[gmx-users] Gmx_solvate

Justin Lemkul jalemkul at vt.edu
Mon Apr 16 13:56:07 CEST 2018

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.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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