[gmx-users] Adding water to specific part of a box

[Neda Rafiee]

Thanks Victor!


----- Original Message -----
From: "Victor Rosas Garcia" <rosas.victor at gmail.com>
To: gmx-users at gromacs.org
Sent: Monday, February 13, 2017 9:30:12 PM
Subject: Re: [gmx-users] Adding water to specific part of a box

You could try resizing the box of your system with gmx editconf, so the box
does not include the region below the bilayer,  add solvent with either gmx
insert-molecules or gmx solvate, and then use gmx editconf again to leave
the box as it was before adding the solvent.

Hope this helps

Victor

2017-02-13 3:17 GMT-06:00 Neda Rafiee <nerafiee at ipm.ir>:

> I mean adding water above the membrane bilayer and not below it for
> example. There is an option in VMD in Selection part, which allows the user
> remove water molecules from z>(upper bond) and z<(lower bond), but I don't
> know if there is any option which allows you insert water molecules like
> that!
>
>
>
> ----- Original Message -----
> From: "Mohamad Koohi-Moghadam" <m.koohi.m at gmail.com>
> To: gmx-users at gromacs.org
> Sent: Monday, February 13, 2017 12:41:10 PM
> Subject: Re: [gmx-users] Adding water to specific part of a box
>
> What do you mean by "specif part"? For example just in binding site of
> protein-ligand and not in other part?
>
> On Mon, Feb 13, 2017 at 5:02 PM, Neda Rafiee <nerafiee at ipm.ir> wrote:
>
> > Dear users,
> > Any one knows how to add water molecules only to specific parts of a
> > system in GROMACS?
> > --
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