[gmx-users] Calculation of dielectric constant

[Saumyak Mukherjee]

Thanks a lot Philip for your suggestion.

On 11 May 2017 at 13:41, Philip Loche <ploche at physik.fu-berlin.de> wrote:

> Hey Saumyak,
>
> g_dipoles applies the formula derived by Neumann (
> http://dx.doi.org/10.1080/00268978300102721), which is proportional to
> 1/V (box volume) and can not applied in your case. According to your
> description you should consider to calculate a dielectric profile around
> your protein. If its spherical take a look at the following paper:
> http://link.aps.org/doi/10.1103/PhysRevE.92.032718 <
> http://link.aps.org/doi/10.1103/PhysRevE.92.032718>
>
> Best
>
> Philip
>
> —
>
> Philip Loche
> Department of Physics
> Freie Universität Berlin
> Arnimallee 14, Room 0.3.30
> 14195 Berlin, Germany
>
> phone: +49 (0)30/838-55279
>
> > On 11. May 2017, at 07:49, Saumyak Mukherjee <
> mukherjee.saumyak50 at gmail.com> wrote:
> >
> > Dear users,
> >
> > I am trying to calculate the dielectric constant of water within a
> certain
> > distance of protein.
> >
> > For this I have generated an ordered trajectory using trjorder. Then I
> have
> > created an index group for an estimated number of water molecules
> (average
> > of the numbers in nshell.xvg generated from trjorder).
> >
> > Thereafter, I have used the g_dipoles program along with the flag -eps to
> > get dielectric constant. But the results are incorrect, as I am expecting
> > the dielectric constant to be greater than 40 or so, but it is showing
> ~3.5.
> >
> > What am I doing wrong? Any help would be highly appreciated.
> >
> > Thanks and regards,
> > Saumyak
> > --
> > ================================
> > *Saumyak Mukherjee*
> >
> > Junior Research Fellow
> > Prof. Biman Bagchi's Group
> > Solid State and Structural Chemistry Unit
> > Indian Institute of Science
> > Bangalore - 560012
> >
> > Mob : 8017292426
> > Alternative e-mail : saumyakmukherjee at gmail.com
> >                                smukherjee at sscu.iisc.ernet.in
> > ================================
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-- 
================================
*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukherjee at gmail.com
                                smukherjee at sscu.iisc.ernet.in
================================