Re: vmd-l: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Mar 23 2018 - 10:59:05 CDT

I don't have specific knowledge regarding that plugin but the issue here is
that the dipole of a charged system is only well-defined within a given
coordinate frame (the math isn't too hard to work out - try shifting all of
the position vectors by an arbitrary constant and see what happens).

Presumably you can script a selection, compute the center of geometry (you
can also try center of mass and center of charge) and then "vecsub" and
"move"/"moveby" in order to transform each frame before using the plugin.

HTH,
BKR

On Thu, Mar 22, 2018 at 7:17 PM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:

> Hi everyone,
>
> I have a question about the dipole plugin. Currently, if I have a charged
> molecule,
> to get its dipole moment is it enough to use this plugin or do I have to
> "subtract the position vector of the geometrical center of the molecule
> times the total charge from the dipole vector and then take the absolute"
> as suggested in
> this post from 2007?
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8857.html
>
> I'm asking because I thought DNA didn't have a net dipole but the dipole
> watcher shows, even when I don't have ions nor water added, a net dipole
> of around 15 Debyes perpendicular to the molecule's axis. If this is true,
> does anybody have a clue of why does the molecule have a net dipole? I've
> been looking for long at the bibliography and, removing water and ions,
> there
> doesn't seem to be any reason for this to happen.
>
> Thank you very much for any clue you may provide me,
>
> Sebastian
>

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