[gmx-users] Dipole correction in PME

David van der Spoel spoel at xray.bmc.uu.se
Tue Sep 20 14:26:14 CEST 2005

On Tue, 2005-09-20 at 14:30 +0300, Janne Hirvi wrote:
> Hello!
> 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
> conductor
> (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?
You did not make a terrible mistake, since many people have made the
same one...

Whether or not to use conducting boundaries is a still under dispute, I
have seen some unpublished work concluding that one should use vacuum
boundary conditions (eps = 1). I have tested this for water systems and
it does make quite a large difference in e.g. the dielectric constant. 

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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