VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Aug 05 2021 - 08:54:20 CDT

The solvation will not know what your system contains. So it will solvate
in all directions.

What you can do is to use VMD select command and select and then delete all
solvent molecules that are not needed. Alternatively you can select
everything except the unwanted solvent molecules and write that out.

On Thu, 5 Aug 2021 at 9:25 PM, Amir Zeb <zebamir85_at_gmail.com> wrote:

> hello vmd users,
>
> I want to solvate the membrane in vmd but the Add Solvation Box solvate it
> in all dimensions like X Y and Z, but as normal practice, the membrane
> should be solvated in Z dimensions only. can someone please guide me how to
> do such solvation of membrane in Z dimensions only in vmd??
>
> Regards
>
> Amir
>