AMBER Archive (2006)

Subject: Re: AMBER: Electrostatic Energy Constant

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Fri Sep 29 2006 - 14:44:25 CDT

>
> Will you please tell me in which condition the
> constant is 332? As we know, the microenviroment of
> the biomolecule is very complex. My understanding is

This is not the dielectric constant, but a conversion factor (i.e.
constant) converting from normal charge units to the appropriate energy
units... Effectively,

E = qi*qj / 4pi*eps0*eps*rij

where "eps" the dielectric constant. The 4*pi*eps0 relates to the
permittivity in free space.

Yes, it is true that the dielectric environment changes as a function of
the surroundings and also that a dielectric constant only has real meaning
as a bulk or aggregate or macroscopic property.

For simulations with explicit water, we hope that the dielectric
environment is represented automatically and we set the dielectric
constant to be 1; calculated dielectric constants for bulk TIP3P are
approximately 60 (compared to 78.3 experimentally) if I remember
correctly. Without explicit water, there have been many modified
dielectric attempts ranging from distance dependent dielectric to
sigmoidal to generalized Born and others. A vast literature; Harvey has
an early article on the effective dielectric in a protein (in Proteins) if
I remember correctly.

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