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

[Zhenyu Meng]

Dear Prof. Groenhof,
Your suggestion sounds enlightening, I can give it a try.
Thank you!

2015-08-05 14:45 GMT+08:00 Groenhof, Gerrit <ggroenh at gwdg.de>:

>
>    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
> Message-ID:
>         <CAJffFwaSp5gHL6pEjvgJyFsJxTdM=
> 9CWGGvOpQ6UpbutaNv1cg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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
> > > --
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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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-- 
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University