From: J.Dziedzic <J.Dziedzic@so...>  20091209 17:49:48

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. When presented with the same system: REMARK 1 Two hydrogen atoms one Bohr apart ATOM 1 H XXX 1 0.000 0.000 0.000 1.00 1.00 ATOM 2 H XXX 1 0.529 0.000 0.000 1.00 1.00 and a simple input file: read mol pqr test.pqr end elec name test mgauto dime 193 193 193 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 elecEnergy test end quit ... 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? Thank you in advance,  J. Dziedzic 