# 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:

- A bug fix in Vacc_molAcc which removed spurious regions of high internal dielectric values
- A switch in the algorithm used to compute the dielectric smoothing for srfm smol
- The addition of the Vacc sphere density (sdens keyword) as a variable and a change in the default sdens value from 3.0 to 10.0

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):

- Translation of contrib/pmgZ library from FORTRAN to C
- Differences in numerical implementations between FORTRAN and C compilers result in small round-off discrepencies
- Small margins due to these round-off discrepencies acumulate in the computations

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