VMD-L Mailing List

From: SHRAVANI NETHI (p20160500_at_hyderabad.bits-pilani.ac.in)
Date: Wed Jul 01 2020 - 10:16:11 CDT

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? 
Any way thanks for the quick response 

-Sravani

Sent from my Huawei phone


-------- Original message --------
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 29 Jun, 2020, 4:43 PM
To: "SHRAVANI NETHI ." <p20160500@hyderabad.bits-pilani.ac.in>
Cc: Vmd l <vmd-l@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@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@gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.