[gmx-users] Calculation of dielectric constant

[Philip Loche]

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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