From: Madhurima Jana (tinni.217_at_gmail.com)
Date: Wed Nov 24 2010 - 05:25:06 CST
Actually, our system is very large so that for protein molecule (around 1000
residues) we want to perform all-atom simulation whereas we want to treat
water molecules as an implicit solvent. So that we want to represent water
molecules by GB or PB model. Is it possible by NAMD?
On Mon, Nov 22, 2010 at 8:37 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, Nov 22, 2010 at 8:48 AM, Madhurima Jana <tinni.217_at_gmail.com>
> > 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.
> > 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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