[gmx-developers] position dependent dielectric constant

Nazish Hoda nazish at umich.edu
Thu Sep 25 18:53:47 CEST 2008

Hi all,


I am trying to incorporate a position dependent dielectric constant.

The dielectric constant will have two different values:

\epsilon = \epsilon_ 1       r < r_c

\epsilon =  \epsilon_2      r > r_c.


I know a simple way of implementing this;

F_new =  F_old (estimated using \epsilon_2)  + 1/(4pi) \sum_{r < r_c}
q_iq_j (1/\epilon_1  - 1/epsilon_2) rij/rij^3.


I looked through the PME code once it looks intimidating. If any one can
help me with this that would be great. I want to know how to access the
variables I need: q_i, q_j, \epsilon_r. Also, I want to do a neighbor
search; how to do efficiently do that in Gromacs (I don't want to write more
inefficient algorithm).  


Thanks, Nazish. 






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