[gmx-users] how to calculate ESP at certain position

[André Farias de Moura]

Dear Zhenyu,

I would be careful with the choice of words: you cannot say that a point in
space has an electrostatic potential without saying where you have set the
reference electrostatic potential to zero (it is a relative quantity, not
absolute).

I never used the spherical version of g_potential myself, but assuming it
does what my lab made code does, you will get a profile of V(r) around the
COM of the reference group and the value at the COM should always be
compared with the values of the surrounding spherical layers, so you will
be able to state that the electrostatic potential is either higher or lower
at that point with respect with a reference position in the radial profile
(your choice).

Also mind that the COM is not an actual point, you are performing a
numerical double integration of the charge density between r and r+dr, so
the COM is actually a small sphere. Being small, I do not think that
instantaneous calculation of electrostatic potential would make any sense
at all, the region around the COM is always the region where the potential
takes longer to converge (tens of nanoseconds in my case). This is not an
artifact of the program: parallel layers along one direction of the box
have the same volume and are sampled with the same statistical precision,
whereas spherical layers have increasing volumes as we move from the COM,
meaning that statistical sampling is very poor at the COM as compared to
the outer layers (I would expect wild oscillations without physical
significance at the origin of the profile).

best

Andre

On Tue, Aug 4, 2015 at 12:58 AM, Zhenyu Meng <fdmm1989 at gmail.com> wrote:

> Dear all,
> I want to calculate electrostatic potential at a certain position in a box.
> I check the available tools and found only g_potential is related with
> this.
> However g_potential give the graph of potential vs. box length(may be z
> axis).
> So my first question: Is this potential value the potential at the COM of
> the group I select?
> Second question: how can I calculate the potential at certain position vs.
> time?
>
> --
> Sincerely,
> Mr. Meng Zhenyu
> Division of Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090