[gmx-users] How to add solvent in a Biphasic Systems ?

[Mark Abraham]

Hi,

On Wed, Jun 15, 2016 at 5:49 AM Jinfeng Huang <wwsshhjjff00 at 163.com> wrote:

> Dear gromacs users,
>
>
>     I want to build a liquid-solid system following the tutorial "Building
> Biphasic Systems" (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
> ), but I have met two problems during my operation.
>
>
>     1) After adding a protein to the liquid layer, the tutorial describe
> as "Then proceed with another round of solvate to add water, as before." I
> don't know how to add the water. I used the "solvate" command and there
> will be a lot of waters added in the solid layer (There are no waters added
> in the solid layer after I changed the value of the C radius when I solvate
> the solid layer only). How should I solvate the protein-solid system
> without waters added in the solid layer?
>

As gmx solvate -h explains, you can exclude regions based on tuning the
radius of the atoms within it. So do that for the solid atoms, perhaps via
some (temporary?) renaming. Or afterwards, use gmx select to choose the
unsuitable water molecules e.g. via particular ranges of coordinate values,
and then editconf to remove that subset.

    2)How to add TIP3P water models with the solvate command in gromacs
> instead of the spc216 water model?
>

They have the same geometry, so you can use either at this stage.

Mark


>    It's highly appreciated if there are any suggestions.
> Jingfeng
>
>
>
>
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