Re: Positional restraints - Dielectric constant

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 02 2011 - 11:39:39 CST

On Wed, Mar 2, 2011 at 11:56 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> (2) What about the dielectric constant for such an ensemble, spanning
> from 1 for the protein (and the lipid ?) and ca 80 for TIP3? Specific,
> authoritative tutorial, such as
> <http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm> do not mention
> dielectric.

i am wondering why people come up with this thing all the time.
it doesn't make any sense at all, if you really thing about it.

a choice of 1 (vacuum) is the proper choice for an all atom simulation
with explicit solvent. the fact that you have a higher dielectric constant
in water, for example, is a _result_ of the calculation (the static DEC
is a measure for the response to local polarization). you only need
to set the dielectric constant for an _implicit_ model, where you
approximate the screening of coulomb interactions by a continuum
model.

for more details i suggest having a look at text books on the
subject, e.g. hansen, macdonald, theory of simple liquids.

cheers,
    axel.

> Thanks for advice
>
> francesco pietra
>
>

-- 
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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