VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jun 29 2020 - 06:13:44 CDT

you need to have something to uniquely identify each layer, e.g. a custom
residue id or segment name.
then you can use the "exwithin" selection keyword with a suitable cutoff.
any atom/molecule matched by an "exwithin" selection of two layers each
combined with the "and" keyword will be between those two layers. something
like: (exwithin 6.0 of segname LY1) and (exwithin 6.0 of segname LY2)

axel.

On Mon, Jun 29, 2020 at 4:34 AM SHRAVANI NETHI . <
p20160500_at_hyderabad.bits-pilani.ac.in> wrote:

> Dear users,
> I have a clay system with waters sandwiched between clay layers and around
> layers.
> The layers are in continuous motion, and the layers are lablled with
> different segnames. the water molecules also have different segname for
> interlayer and surrounding water. The water molecules continuously move
> from solvation shell and interlayer region. Hence, I would like to see the
> motion of water molecules only between the interlayers through out
> trajectory where the interlayer region is dynamic.
> Help *me to select region between these dynamic layers *so that I can add
> other keywords to this.
>
> -sravani
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.