[gmx-users] Inhomogeneity of water molecules insertion into the box

[Justin Lemkul]

On Mon, Apr 1, 2013 at 7:55 AM, Zhikun Cai <caizkun at gmail.com> wrote:

> Hi all,
>
> I would like to add 484 water molecules into the box using command:
>
>  genbox -cp newbox.gro -cs tip4p.gro -maxsol 484 -p topol.top -o
> solvated.gro
>
>
> What I expected is those water molecules would be randomly inserted into
> the box and the box should appear homogeneous. But the result disappointed
> me. Throught VMD, I found that the 484 water molecues was inserted almost
> in one half of the box. Then when I added more water molecules, they began
> to occupy the other half box.
>
> So what could I do to make the inserted 484 water molecules randomly
> positioned in the box in the beginning?
> Your advice would be highly appreciated.
>
>
The -cs solvation mechanism adds solvent in a grid-based approach, so the
outcome you report is exactly what is expected. If you want random
insertion of a certain number of solvent molecules, then you should use the
-ci -nmol option, providing the coordinate file of a single water molecule
to the -ci flag.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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