Thanks a lot Philip for your suggestion. On 11 May 2017 at 13:41, Philip Loche <plo...@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.saumya...@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 : saumyakmukher...@gmail.com > > smukher...@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-requ...@gromacs.org. > > -- > 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-requ...@gromacs.org. -- ================================ *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 : saumyakmukher...@gmail.com smukher...@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-requ...@gromacs.org.