From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Sun Mar 25 2018 - 20:31:45 CDT
Thanks for your suggestion! I tried that and I still get a dipole, but I
noticed from publications that, according to the CHARMM force field, DNA is
polarizable due to asymmetries between the different bases that form each
On Fri, Mar 23, 2018 at 11:59 AM, Brian Radak <brian.radak_at_gmail.com> wrote:
> 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.
> 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
>> 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?
>> 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,
>> doesn't seem to be any reason for this to happen.
>> Thank you very much for any clue you may provide me,
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