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?
http://lists.gromacs.org/pipermail/gmx-users/2004-March/009650.html
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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