From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 09 2009 - 07:22:35 CST
On Mon, Nov 9, 2009 at 7:22 AM, Rajiv Abhyankar
<rajiv.abhyankar_at_gmail.com> wrote:
> Dear All,
> I am doing an SMD calculation on a protein solvated in water box. I want to
> know what dielectric constant I should assign to my system-1 as for vacuum
> or 80 as for water.The reason for my confusion is that I feel that if I
> assign a value of 80, the even those charges that are not in the water
dear rajiv,
perhaps you should first consider what changing the value of the dielectric
constant does: it will scale down _all_ electrostatic interactions. this only
makes sense, if you have no solvent and want to (crudely) simulate the
effect of a solvent in a continuum approach.
axel.
> environment but are in the protein environment will be affected and will
> give a wrong value of the electrostatic energy.
> Rajiv
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.
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