AMBER Archive (2006)

Subject: Re: AMBER: DIELC?

From: backy (backy_at_ibms.sinica.edu.tw)
Date: Sat Aug 19 2006 - 03:04:14 CDT

Hello, dac:
I also have a question about the electrostatic energy calculations in AMBER.
As minimizing (with GB method) a protein with about 100 steps, I found that
those electrostatic terms (EEL, 1-4 EEL and EGB ) rapidly converged although
the total energy is not fully stabilized.
What is the basis for this kind of situation?

Thanks. :)

backy

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Monday, August 14, 2006 12:43 AM
Subject: Re: AMBER: DIELC?

> 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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