[gmx-users] Gmx_solvate

[Justin Lemkul]

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?

No.

> 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

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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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