GROMACS version: 2019.3
GROMACS modification: No
Dear gromacs users,
I am running simulations of a protein in pure methanol.
I was wandering what is the meaning of epsilon-r in the mdp file. Looking at the manual, it is defined as :
(1) The relative dielectric constant. A value of 0 means infinity.
So I would say it is the relative dielectric constant (dielectric_constant_medium/dielectric_constant_vacuum) and I should use the one reported in literature for the methanol at the given temperature of my sims. My concern is the following, why when we run sims in water, don’t we use epsilon-r = 80 but epsilon-r = 1? is there some kind of implicit normalisation that I am missing?
Thanks in advance for your help,
Emiliano De Santis