AMBER Archive (2000)

Subject: Re: dielectric constant

From: Soaring Bear (bear_at_dakotacom.net)
Date: Sat Aug 19 2000 - 10:03:43 CDT

There is a whole body of literature on this question.
You might start with:

Daggett V. Kollman PA. Kuntz ID. Molecular dynamics simulations of small
peptides: dependence on dielectric model and pH. Biopolymers 31:285-304
1991

Soaring Bear Ph.D. Research Pharmacologist
Scientific advisor to the health professions
http://soaringbear.com
soaringbear_at_yahoo.com 

--
HERBMED is Science Mag. hotpick for June 23, 2000
http://www.sciencemag.org/cgi/content/summary/288/5474/2091b
http://www.amfoundation.org/herbmed.htm

----- Original Message -----
From: David Small <David.Small_at_hec.utah.edu>
To: <amber_at_cgl.ucsf.edu>
Sent: Thursday, August 17, 2000 12:10 PM
Subject: dielectric constant

>
> Hi,
>
> I've been doing simulations (sander, gibbs) with the default
> dielectric constant of 1 (DIELC = 1).  I've read that the dc of water is
> around 78, and being that my system is solvated in water, running with a
> DC of 1 would produce incorrect results (I have seen quite varied
> results as I alter DIELC).  If I don't already have the correct DC from
> data, how would I find an representative value to use?
>
> thanks,
>
> dave
>
>