README for solv APBS examples

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 1.4-binary -36.2486 -390.4122 -354.1635 -35.595 -390.023 -354.424
1.4 -36.2486 -390.41223 -354.1635
1.3 -36.2486 -390.4121 -354.1635
1.2.1 -36.2486-390.4121-354.1635
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 1.4.1-binary -37.5759 -391.2389 -353.6629 -35.595 -390.023 -354.424
1.4 -37.57593 -391.23893 -353.6629
1.3 -37.5760-391.2388-353.6629
1.2.1 -37.5760-391.2388-353.6629
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.

3 The discrepancy in values between versions 1.3 and 1.4 is most likely due to the following factor(s):

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