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

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Sun Mar 25 2018 - 20:31:45 CDT

Hi Brian,

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
base pair.

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.
>
> 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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