VMD-L Mailing List

From: SHRAVANI NETHI . (p20160500_at_hyderabad.bits-pilani.ac.in)
Date: Wed Jul 01 2020 - 12:04:05 CDT

The cutoff distance is selected as 8 angstrom as they layers moved max of 8
ang apart by the end of simulation thpugh initially they were placed 4 ang
apart.
-Sravani

---------- Forwarded message ---------
From: SHRAVANI NETHI . <p20160500_at_hyderabad.bits-pilani.ac.in>
Date: Wed, 1 Jul, 2020, 10:29 PM
Subject: Fwd: Fw: vmd-l: selection of molecules in dynamic region
To: vmd-l <vmd-l_at_ks.uiuc.edu>

Thank you for the clarification sir.
One more problem i observed during the selection is the water molecules
which are not lying exactly between layers also getting selected as they
fall within common cutoff distance from both reference points diagonally
but not horizontally (along Z direction) .
Hence, I am getting extra water molecules in XY plane, the region parallel
to reference clay layers, which lie at bit far away from expected plane.
The command i used is
*same residue as resname SPC and ((exwithin 8 of segname CLY1) and
(exwithin 8 of segname CLY2))*

Where interlayer water (with segname W1) and solvation water (with segname
W) have common resname SPC,
layer 1 and 2 have segname CLY1 and CLY2 respectively.
To avoid these extra waters, i used range of x and y coordinates in
addition to above command.
Is there any other way out??
 Thanks in advance.
-Sravani

---------- Forwarded message ---------
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Date: Wed, 1 Jul, 2020, 9:23 PM
Subject: Re: Fw: vmd-l: selection of molecules in dynamic region
To: SHRAVANI NETHI <p20160500_at_hyderabad.bits-pilani.ac.in>
Cc: vmd-l <vmd-l_at_ks.uiuc.edu>

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.