From: Gatti, Domenico <dgatti@me...>  20091211 15:54:10

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: 3135770620 or 3139934238 Fax: 3135772765 dgatti@... 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, 20091209 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 520, 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 selfinteraction 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 selfenergies: > > 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 