README for solv APBS examples

$Id: README.html 1440 2009-11-17 20:37:08Z yhuang01 $

The example input files in this directory calculate the solvation energies of methanol and methoxide.

The source for this example is UHBD.

Input File Description APBS Version Results (kJ/mol) UHBD (kJ/mol)
Methanol Methoxide Difference Methanol Methoxide Difference
apbs-mol.in Focusing to 0.25 A, srfm mol 1.2.1 -36.2486 -390.4121 -354.1635 -35.595 -390.023 -354.424
1.22 -36.2486-390.4121-354.1635
1.1.0 -36.2486-390.4119-354.1632
1.0.0 -36.2486-390.4119-354.1632
0.5.1 -36.2486-390.4119-354.1632
0.5.0 -36.2486-390.4119-354.1632
0.4.0-36.2486-390.4119-354.1632
apbs-smol.in Focusing to 0.25 A, srfm smol 1.2.1 -37.5760 -391.2388 -353.6629 -35.595 -390.023 -354.424
1.22 -37.5760-391.2388-353.6629
1.1.0 -37.5760-391.2387-353.6627
1.0.0 -37.5760-391.2387-353.6627
0.5.1 -37.5760-391.2387-353.6627
0.5.0 -37.5760-391.2387-353.6627
0.4.01-37.5760-391.2387-353.6627
0.3.2-36.2486-390.4119-354.1632
0.3.1-36.2486-390.4119-354.1632
0.3.0-36.2486-390.4119-354.1632
0.2.6-36.2486-390.4119-354.1632
0.2.5-36.2486-390.4119-354.1632
0.2.4-36.2486-390.4119-354.1632
0.2.3-36.2223-391.7995-355.5771
0.2.2-36.2223-391.7995-355.5771
0.2.1-36.222-391.800-355.577
0.2.0-36.222-391.800-355.577
0.1.8-36.222-391.800-355.577

1 The discrepancy in values between versions 0.4.0 and 0.3.2 is most likely due to three factors:

2 APBS 1.2 has switched the multigrid smoothing algorithm from standard Gauss-Seidel to Gauss-Seidel red/black in order to facilitate parallelization. This switch has caused small differences in individual calculation energies which, when combined to the final answer, create larger errors (up to 0.04%). These errors can be reduced by resetting the APBS error tolerance to 1e-9 or smaller values. For a more detailed explanation, please see here.

Please see the ChangeLog or the APBS documentation for more information.