[gmx-users] Calculation of dielectric constant
ploche at physik.fu-berlin.de
Thu May 11 10:11:20 CEST 2017
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>
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 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users