VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jul 01 2020 - 10:53:37 CDT

On Wed, Jul 1, 2020 at 11:43 AM SHRAVANI NETHI <
p20160500_at_hyderabad.bits-pilani.ac.in> wrote:

> Dear Axel sir,
> Your suggestion helped me... But i could not get the difference between
> using within and exwithin.
> How they are different? I tried with the commands but could not find
> difference visually.
> How do they differ?
>

both selections look for particles within a given distance from the
reference particles. the within selection includes the reference, the
exwithin selection does not include them. with the kind of operation you
want to do, it is advisable to make your (ex)withinc cutoff large enough to
occasionally also include particles from the neighboring layer, or else you
may miss some. when you use within, those atoms will be in both selections
and thus will be shown, using exwithin will avoid that. using a shorter
cutoff may make you miss atoms that should be selected. in the end it all
depends on the specifics of your system and how flexible/mobile it is.

axel.

> Any way thanks for the quick response
>
> -Sravani
>
> Sent from my Huawei phone
>
>
> -------- Original message --------
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Date: Mon, 29 Jun, 2020, 4:43 PM
> To: "SHRAVANI NETHI ." <p20160500_at_hyderabad.bits-pilani.ac.in>
> Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: selection of molecules in dynamic region
>
> 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.
>
> 

-- 
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.