Re: AMBER: dielectric constant for blends

From: David A. Case <>
Date: Mon, 8 Sep 2003 08:23:34 -0700

On Mon, Sep 08, 2003, Taner E. Dirama wrote:

> I am doing NPT MD simulations of trhalose and glycerol (no water) at
> different compositions using Amber7. Knowing the significant effect of
> dielectric constant on many properties, how would you think that it should
> be taken into account for blends? Is there a way of estimating the dilectric
> constant for blends?

One generally assumes that the physical features that lead to dielectric
behavior are included in explicit MD calculations. Hence, there is no need
to separately use any dielectric other than 1.

You can compute the dielectric of your mixtures by analyzing the fluctuations
in the dipole moments of the sample. As far as I know, there is no
already-programmed way in Amber to do this -- you would have to write some
analysis code for yourself.

Of course, I am not familiar in any detail with the literature on such
nonaqueous systems, so you probably should also study what other people do
when simulating these systems.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Mon Sep 08 2003 - 16:53:06 PDT
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