[gmx-users] Dielectric constant calculation with Gromacs-3.3.1
lugodmer at gmail.com
Fri Mar 9 19:47:26 CET 2012
I am going to calculate the dielectric constant of rigid water model, but I
am not quite sure about the use of boundary condition. I know there is an
option "epsilon_surface", and its default number is 0. I am using PME to
calculate electrostatic interaction. From the literature and the mailing
list, it seems there are 2 following options:
1. set epsilon_surface to be its default value 0, and use g_dipoles to
calculate the dielectric constant.
2. set epsilon_surface to be inf (someone calls this conducting boundary
condition), and use g_dipoles to calculate the dielectric constant. Here I
am not sure which option I should use. epsilon_RF seems just to work with
reaction field method, not PME. But I don't see any option for PME.
And I am not sure what formula is used for the dielectric constant in
Let a = (4*pi*<M^2>) / (3*k*T*V) in Gaussian unit assuming <M>=0
For case 1: it seems to be: epsilon = 1/(1-a)
For case 2: it seems to be: epsilon = 1+a
And finally I think these two cases (epsilon_surface in MD and
corresponding formula) should give very close answer. But I am not sure
which way is better. Could any one please help me sort this out? And I am
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