Re: Different Dielectric constant value for different segment

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 22 2010 - 09:07:06 CST

On Mon, Nov 22, 2010 at 8:48 AM, Madhurima Jana <tinni.217_at_gmail.com> wrote:
> Hi,
>
> We want to perform MD simulation of a protein in aqueous solution using
> NAMD. We want to know that if it is possible to define a particular
> dielectric constant value for some segments and another value for other
> segments. Is it possible in NAMD?

not this is not possible. and it would be _very_ inconsistent.

what would be the reasoning behind this?

because what a different (static) dielectric constant would
amount to is effectively a rescaling of the charges.
in other words, you would change your force field.

axel.

> Any suggestion is highly acceptable,
> thanks,
> madhurima
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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