Re: [Apbs-users] Example script of grid artifact subtraction

[Nathan B. <ba...@bi...>]

Hello --

Actually, all of the input files provided in the APBS examples/ directory
demonstrate this in a variety of ways.  Some of the examples remove
self-energies by calculating solvation energies while other examples remove
self-energies by using exactly the same grid positions for all atoms in each
part of the calculation.

Hope this helps,

Nathan

On Fri, Dec 11, 2009 at 9:23 AM, Gatti, Domenico <dg...@me...>wrote:

> Hi All,
>    Could we post an EXAMPLE SCRIPT of how the corrections suggested by
> Gernot and Nathan for Dziedzic's simple calculation of two point charges
> should be implemented? Does this mean that the grid artifact subtraction
> should be carried out always in all the APBS calculations? Perhaps, this
> occurs already by default, and I did not realize it.
> Best,
> Domenico
>
>
> Domenico Gatti
> Biochemistry & Mol. Biology
> Wayne State University School of Medicine
> 540 E. Canfield Avenue
> Detroit, MI 48201
> Tel: 313-577-0620 or 313-993-4238
> Fax: 313-577-2765
> dg...@me...
>
>
>
>
>
>
> Hi All --
>
> Gernot is absolutely correct.  I would also add that, after correcting the
> issues Gernot raised below, you should also examine the sensitivity of your
> results on "chgm spl0" vs. "chgm spl2" since charge discretization can
> affect these types of calculations as well.
>
> Thanks,
>
> Nathan
>
> On Dec 10, 2009, at 9:31 AM, Gernot Kieseritzky wrote:
>
> > Hi!
> >
> > On Wed, 2009-12-09 at 17:49 +0000, J.Dziedzic wrote:
> >> Hi!
> >>
> >>   I am confused about the result of a very simple calculation when done
> >> with APBS. Consider a trivial system of two point charges with unit
> >> charges at a separation of 1 Bohr length, in vacuum. The Coulombic
> >> energy of this system is exactly 1 Hartree, that is 2625.5 kJ/mole.
> >> ...
> >> ... APBS yields 31740 kJ/mole, which off by a factor of 12. Making the
> >> grid finer only makes things worse, the results being:
> >>
> >> dime   Energy (kJ/mole)
> >> 65     1.209E04
> >> 129    2.222E04
> >> 193    3.174E04
> >> 257    4.058E04
> >> 289    4.539E04
> >>
> >>   which are all way off, by a factor of 5-20, from the correct value of
> >> 2625.5 kJ/mole.
> >>
> >>   I understand that normally one is interested in energy differences
> >> between a system in vacuo and a solvated system, and any discretization
> >> errors introduced are canceled if the grid is the same in both
> >> calculations. Yet, with a system so trivial, without any dielectric
> >> at all and, thus, without the arbitrariness of the cavity, what is the
> >> underlying reason for the calculation being so off from the mark?
> >
> > Two words: grid artefact! Basically, the deviation is not due to
> > numerical problems, rather the high energy values you observe are the
> > result of the self-interaction of the grid points. That's why the
> > deviation is increasing with higher resolution as the grid points are
> > getting closer. What you have to do to get the total electrostatic
> > energy of your system without self-energies:
> >
> > 1) Compute the Coulomb energy in the homogeneous continuum.
> >
> > 2) Compute the solvation energy of the same charge distribution using
> > APBS. The grid artefact cancels as you calculate an energy difference
> > here. This, of course, requires that you use the same grid setup in both
> > APBS runs.
> >
> > 3) Add the values together.
> >
> > Best regards,
> > Gernot Kieseritzky
>
>
>
>
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-- 
Nathan Baker (http://bakergroup.wustl.edu)
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis