AMBER Archive (2006)

Subject: Re: AMBER: DIELC?

From: David A. Case (case_at_scripps.edu)
Date: Sun Aug 13 2006 - 11:43:58 CDT

On Sat, Aug 12, 2006, backy wrote:
>
> Does that mean as running energy minimizations based on GB, the EEL term
> would not have any changes no matter setting any DIELC values?

Yes.

> Then, what is the really using value of dielectric constants for calculating
> the electrostatic interactions (EEL) between the protein's parts in GB?

Dielectric constants play a key role in continuum solvent theory, but the
input variables "intdiel" and "extdiel" are used there. (See p. 120 of the
Users' Manual.) Note that in GB, the value of EEL is the raw Coulomb
interaction (i.e., as if the dielectric were intdiel, which is usually unity);
all of the screening effects of the continuum solvent are included in the EGB
value. But only the sum EEL + EGB has any real meaning: the division into
the two parts is rather arbitrary.

...hope this helps...dac
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