[gmx-users] What is epsilon_r?

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 16 23:28:03 CEST 2012

Andrew DeYoung wrote:
> 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?




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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