[gmx-users] dipole correction in 3.1-beta

[David L. Bostick]

HI Erik,

Thanks for responding.  Ok, I'm glad we agree on the equations.  The slab
ewald is not a true 2D ewald, so there are no changes necessarry for the
current pme.. just the addition of that extra term dependent on the z
component of M.  It is a "poor man's" version that involves the extension
of the z dimension of the simulation box, but it produces really good
results.  True 2D sums with 3D periodicity are just now getting there.
There is a recent paper if you're interested:

J. Chem. Phys. Vol 116, No. 8, 22 Feb. 2002 pp.3430-3438

Once again, thanks,
David

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David Bostick					Office: 262 Venable Hall
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Program in Molecular and Cellular Biophysics 
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On Thu, 21 Feb 2002, Erik Lindahl wrote:

> 
> Hi,
> 
> 
> >
> >   else if(epsilon_surface > 0)
> >     dipole_coeff=2*M_PI*ONE_4PI_EPS0 / (2*epsilon_surface + 1) / vol;
> >   else if(epsilon_surface < 0)
> >     dipole_coeff=2*M_PI*ONE_4PI_EPS0 / vol;
> >
> > this way I can do a simulation in slab geometry if I choose
> > epsilon_surface < 0... say -1.0.  I think there may be an extra 2 in the
> > numerator rather than only  M_PI*ONE_4PI_EPS0 that you mention.  It seems
> > that all the literature I find gives the formulae in Gaussian.. so to
> > convert, I guess we have to multiply by ONE_4PI_EPS0.  Check on this..
> >
> 
> Not necessary - we've already arrived at the same formula; the reason I didn't
> have the 2 in the numerator was that we I divided by 1.5 instead of 3.
> (2*epsilon+1 when epsilon==1).
> 
> 
> >
> > See:
> > J. Chem. Phys., Vol. 109, No. 18, 8 November 1998
> > and
> > J. Chem. Phys., Vol. 111, No. 7, 15 August 1999
> >
> > The second one has the slab geometry correction in it by Berkowitz and Yeh.
> > You may want to include this in the 3.1 release in case somebody wants to
> > use it, but thats up to I guess you and others to decide.
> 
> No problem, the only reason we haven't included more references is laziness -
> it's better the more we have since you avoid the hassle of looking it up in a
> previous paper... I'll add it for 3.1.
> 
> >
> >
> > Please, If you can take a look at this and tell me what you think.  Is
> > there anything I can change?
> >
> 
> No, everything looks really good, apart from the slab thing that I haven't used
> myself. I could of course add it, but since neither David or I work a lot with
> dipole corrections it might be better if you tried it on a test system (where you
> know what to expect :-), and just send me a diff (or the entire file) to avoid
> more typos, and finally get the corrections right?
> 
> Actually, if this means slab geometries are working (is there any change needed
> in the main pme routines?) it's probably better to add a real ewald_geometry
> option that is either 3d or 2d, or maybe you have a better name for it.... The
> sign thing works, but it's not that intuitive :-)
> 
> Cheers,
> 
> Erik
> 
> 
>