VMD-L Mailing List
From: Sam Wallace (sam.wallace_at_adelaide.edu.au)
Date: Tue Aug 28 2012 - 01:35:19 CDT
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- Maybe in reply to: Bhanita Sharma: "RDF COM"
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Hi Bhanita
I had this problem earlier. I overcame it by writing a couple of
scripts. The first adds extra atoms to a trajectory by duplicating it.
It's based off one of Axel's topotools plugins. The second then
assigns the position of those atoms to the centre of mass of a
selection.
if you load this script
https://www.dropbox.com/s/s88u8wm44jpqzjg/RDFcom.tcl
and then call
assign_com molid "selection text 1" "selection text 2"
It will duplicate your trajectory and create two dummy atoms at the
centre of mass of your selections.
Some notes: molid has to be a number, top doesn't work and I haven't
bothered to fix that yet. As it's duplicating the trajectory, you need
to ensure you aren't using a trajectory that is larger than half of
your available RAM or you'll probably run into issues.
You can modify the assign_com process to create additional dummy atoms
at the centre of masses of more selections if you wish. It's not too
much work to do so
-Sam
--------------------------------------------------------------
Sam Wallace, Ph.D Student
School of Chemistry and Physics, University of Adelaide
Adelaide, South Australia 5005, Australia
Phone: +61-(0)8-8303-4332
Fax: +61-(0)8-8303-4358
Email: sam.wallace_at_adelaide.edu.au
"I suppose you wouldn't have a problem with me saying the fermi-dirac
distribution is a soup kitchen"
Date: Thu, 23 Aug 2012 10:58:56 +0530
From: Bhanita Sharma <bhanita123_at_gmail.com>
Subject: vmd-l: RDF COM
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Hi,
I want to calculate the radial distribution function from the center
of mass of a non spherical molecule. How can I do that..? Please help me in
doing this..
Thanks a lot in Advance,
Bhanita Sharma
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Content-Transfer-Encoding: quoted-printable
Hi,<br>=A0=A0=A0=A0 I want to calculate the radial distribution function fr=
om the center of mass of a non spherical molecule. How can I do that..? Ple=
ase help me in doing this..<br><br>Thanks a lot in Advance,<br>=A0
<br>Bhanita Sharma<br>
- --bcaec554d94cc844fe04c7e82263--
- Next message: John Stone: "Re: obtaining the axis of a helix"
- Previous message: Sam Wallace: "Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda)"
- Maybe in reply to: Bhanita Sharma: "RDF COM"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]