[gmx-users] What is epsilon_r?

[Andrew DeYoung]

Hi,

What is the parameter epsilon_r mentioned in the manual
(http://manual.gromacs.org/current/online/mdp_opt.html#el)?  The manual says
that it is the relative dielectric constant.  My initial thought was that
this would only be relevant for reaction-field electrostatics, or somewhere
where implicit solvent is used.  However, it seems that epsilon_rf (not
epsilon_r) is used for reaction-field purpose.

I am not using implicit solvent in my system, nor am I using a
reaction-field method (I am using PME electrostatics); in my system, I am
using an all-atom description.  Then, does epsilon_r generate "additional"
dielectric, beyond what naturally arises from the all-atom description of
the solvent?  

Even though I am not using a reaction-field method, epsilon_r is clearly
affecting something, because when I use g_potential to calculate the
electric potential, the results vary considerably depending on the value of
epsilon_r that I use in my .mdp file.

Do you have any thoughts about what epsilon_r does in an all-atom descripton
of a solvent?  Does it provide "additional" charge screening?

Thank you kindly!

Andrew DeYoung
Carnegie Mellon University