[gmx-users] dipole correction in 3.1-beta
David L. Bostick
dbostick at physics.unc.edu
Fri Feb 22 17:39:51 CET 2002
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 Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
On Thu, 21 Feb 2002, Erik Lindahl wrote:
> > 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 :-)
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