[gmx-users] Gmx_solvate

[rose rahmani]

But the box size is 4 4 12 and i should make an index for about 2000 SOL.
Is there any better solution?


On Mon, 16 Apr 2018, 17:34 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> 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, <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
> >> 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
> >>
> >> --
> >> ==================================================
> >>
> >> 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
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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