rose.rhmn93 at gmail.com
Mon Apr 16 14:51:49 CEST 2018
Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i dont
So trjorder can fix the rest, yes?
On Mon, 16 Apr 2018, 16:26 Justin Lemkul, <jalemkul at 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
> > 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
> > from z=0 of box.
> > I mean when i extract wall and sheet from my last simulation and open it
> > 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
> > 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
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users