[VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Thu Mar 22 2018 - 18:17:30 CDT

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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