[gmx-users] how to calculate ESP at certain position
fdmm1989 at gmail.com
Wed Aug 5 04:00:14 CEST 2015
Thanks a lot for your advice.
I ask this question because I read a related paper which use point-charge
potential: Φ=4πεΣqi/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:
2015-08-04 21:30 GMT+08:00 André 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
> 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).
> 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
> > 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
> > 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
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Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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