On 4/16/18 8:51 AM, rose rahmani wrote:
Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i dont
need them?
Yes.
So trjorder can fix the rest, yes?
No, but trjconv can save what you want based on an index group from gmx
select.
-Justin
On Mon, 16 Apr 2018, 16:26 Justin Lemkul, <jalem...@vt.edu> wrote:
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.
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Virginia Tech Department of Biochemistry
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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