[gmx-users] Dipole correction in PME

Janne Hirvi janne.hirvi at joensuu.fi
Tue Sep 20 13:30:38 CEST 2005


I have been using PME for a while for bulk polymer systems without any dipole
correction (surface_epsilon = 0) and now I wondering about the consequences of
using this default value. If I have understood right, the external dielectric
continuum as vacuum (surface_epsilon = 1) would lead to dipolar layer on the
surface of the sphere next to the continuum, while for the sphere in a
(surface_epsilon = 0) there wouldn't be such a layer. So using a real relative
permittivity for the polymer could be important, but on the other hand "most"
of the force fields have been designed for the relative permittivity of vacuum.

So what would have been the best alternative and have I been making terrible
mistakes using the default value?

How should I proceed when I simulate polymer surfaces with ewald_geometry = 3dc
and large box dimension in z-dimension? Then in the real case I should have in
x- and y-dimensions the permittivity of polymer, but in z-dimension the
permittivity of vacuum. Besides the manual informs that the value of
surface_epsilon doesn't affect on the correction applied in the z-dimension. 

I would thank very much any help or comments.


Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2513326 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi

More information about the gromacs.org_gmx-users mailing list