From: Gernot Kieseritzky <gernotf@ch...>  20091211 17:43:27

Hi! Based on Dziedzic's example: read mol pqr test.pqr end elec name test_inhom mgauto dime 65 65 65 nlev 4 cglen 50 50 50 fglen 12 12 12 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl mdh pdie 1.0 sdie 80.0 chgm spl2 srfm smol swin 0.3 srad 1.4 sdens 10.0 temp 298.15 calcenergy total calcforce no end elec name test_hom mgauto dime 65 65 65 nlev 4 cglen 50 50 50 fglen 12 12 12 cgcent mol 1 fgcent mol 1 mol 1 lpbe bcfl mdh pdie 1.0 sdie 1.0 chgm spl2 srfm smol swin 0.3 srad 1.4 sdens 10.0 temp 298.15 calcenergy total calcforce no end print energy test_inhom  test_hom end quit where test.pqr is ATOM 1 H XXX A 1 0.000 0.000 0.000 1.000 1.000 ATOM 2 H XXX A 1 0.529 0.000 0.000 1.000 1.000 Result (APBS 1.1): test_inhom  test_hom = 2497.9 kJ/mol. For the total electrostatic energy we've got to add the Coulomb energy with sdie=pdie=1. In his example we have: Ec = 1 Hartree = 2625.5 kJ/mol. (You can also use the "coulomb.c" program in the APBS tools directory of the source tar ball). So we obtain for the total electrostatic energy with sdie=80 and pdie=1: E = 2625.5  2497.9 kJ/mol = +127.6 kJ/mol. When sdie approaches 1, E should tend to the Coulomb's law result 2625.5 +/ numerical error (in the order of 1E13), because test_inhom  test_hom vanishes in the limit. Best regards, Gernot On Fri, 20091211 at 10:23 0500, Gatti, Domenico 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: 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 > > > >  > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/googledev2dev > _______________________________________________ > apbsusers mailing list > apbsusers@... > https://lists.sourceforge.net/lists/listinfo/apbsusers 