[gmx-users] Dipole correction in PME

[David van der Spoel]

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have seen some unpublished work concluding that one should use vacuum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.
________________________________________________________________________
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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