[gmx-users] About EWD3DC in Gromacs 3.3 Beta (9.9.2005)

[David L. Bostick]

Hello again,

I didn't write this code, but let me comment..

The new code looks like it is a generalization of the old code.  The
default value for fr->epsilon_r is probably unity. Thus, the two versions
of the code are equivalent.  There is probably an option in the mdp file to
change the dielectric constant of the medium inside the box, which would
change fr->epsilon_r.  This is of course independent of the value of the
dielectric constant of the medium outside the lattice sum (at infinity),
which is labelled "epsilon_surface." Please, someone correct me if I'm
wrong.

David


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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
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On Wed, 21 Sep 2005, Janne Hirvi wrote:

> Hello!
>
> I installed Gromacs version dated on 9.9.2005 and looked at code ewald_util.c,
> which was corrected by Berk Hess from the version 3.2. I am not programmer so I
> don't quite get the meaning of fr->epsilon_r, but even I think how hard I
> can't
> fit these equations of dipole_coeff to those in article of Yeh and Berkowitz.
>
> For case EWD3D:
>
> Code:
> dipole_coeff = 2*M_PI*ONE_4PI_EPS0/((2*epsilon_surface + fr->epsilon_r)*vol);
>
> Article:
> dipole_coeff = 2*M_PI*ONE_4PI_EPS0/((2*epsilon_surface + 1)*vol);
>
> and
>
> for case EWD3DC:
>
> Code:
> dipole_coeff = 2*M_PI*(ONE_4PI_EPS0/fr->epsilon_r)/vol;
>
> Article:
> dipole_coeff = 2*M_PI*ONE_4PI_EPS0/vol;
>
> I can't get original publication of Smith, so the last one might be for vacuum
> case or should it really be independent from permittivity. However equations
> from the article of Yeh and Berkowitz equal to the code of version 3.2, which
> had some other errors (if I understood right).
>
>
> Thanks for any comments!
>
> Janne
>
> -----------------------------------------------------------------------------
> 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
> -----------------------------------------------------------------------------
>
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