[gmx-users] how to calculate ESP at certain position (Zhenyu Meng)

[Groenhof, Gerrit]

   5. Re: how to calculate ESP at certain position (Zhenyu Meng)
   
Haven't given it much thought, but if it is only one or few locations you're interested in, can't you simply place a +1 e charged dummy atom at that location in your system and re-compute the total electrostatic energy?

To correct for the self interaction of that probe charge, you could subtract the total electrostatic  energy of the point charge alone in the same periodic box.

Gerrit




M
Message: 5
Date: Wed, 5 Aug 2015 10:00:10 +0800
From: Zhenyu Meng <fdmm1989 at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] how to calculate ESP at certain position
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        <CAJffFwaSp5gHL6pEjvgJyFsJxTdM=9CWGGvOpQ6UpbutaNv1cg at mail.gmail.com>
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Dear Andre,
Thanks a lot for your advice.
I ask this question because I read a related paper which use point-charge
potential: ?=4???qi/ri .
I'm very curious about how it could fulfill this since they mention they
use GROMACS but according to my knowledge GROMACS does not have such a tool.
So I suppose they write their own code.
Here is the link of the paper:
http://pubs.acs.org/doi/abs/10.1021/jp803661f



2015-08-04 21:30 GMT+08:00 Andr? Farias de Moura <moura at ufscar.br>:

> 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
> > --
> > Gromacs Users mailing list
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>
>
> --
> _____________
>
> Prof. Dr. Andr? Farias de Moura
> Department of Chemistry
> Federal University of S?o Carlos
> S?o Carlos - Brazil
> phone: +55-16-3351-8090
> --
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--
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University


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