Hi~ 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 Gromacs: 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 using Gromacs-3.3.1. Thanks, Liang
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
