# README for Born APBS examples

This is the canonical electrostatics test case: Born ion. A non-polarizable ion with a single embedded point charge; has an analytical solution for the potential. We examine the solvation free energy as a function of ionic radius.

Please see apbs.in for details on the particular solvation energy calculations. Analytical results are given in pmf.dat.

This example was contributed by Nathan Baker.

Input File | Description | APBS Version | Results (kJ/mol) | Analytical (kJ/mol)
--- | --- | --- | --- | ---
apbs-mol-auto.in | Sequential, 3 A sphere, 3-level focusing to 0.188 A, srfm mol | 1.4.1-binary | -229.7736 | -230.62
1.4 | -229.77363
1.3 | -229.7735
1.2.1 | -229.7735
1.2 | -229.7735
1.1.0 | -229.7735
1.0.0 | -229.7735
0.5.1 | -229.7735
0.5.0 | -229.7735
0.4.0 | -229.77351
0.3.2 | -229.7248
0.3.1 | -229.7248
0.3.0 | -229.7248
0.2.6 | -229.7248
0.2.5 | -229.7248
0.2.4 | -227.1859
0.2.3 | -227.1589
0.2.2 | -227.186
0.2.1 | -227.19
0.2.0 | -227.19
0.1.8 | -227.19
apbs-smol-auto.in | Sequential, 3 A sphere, 3-level focusing to 0.188 A, srfm smol | 1.4.1-binary | -229.0124 | -230.62
1.4 | -229.0124
1.3 | -229.0124
1.2.1 | -229.0124
1.2 | -229.01242
1.1.0 | -229.0123
1.0.0 | -229.0123
0.5.1 | -229.0123
0.5.0 | -229.0123
0.4.0 | -229.0123
apbs-mol-parallel.in | Parallel with 4 processors, 3 A sphere, focusing to 0.103 A, srfm mol | 1.4.1-binary | -230.49184 | -230.62
1.4 | -230.49193
1.3 | -230.4918
1.2.1 | -230.4918
1.2 | -230.49182
1.1.0 | -230.4916
1.0.0 | -230.4916
0.5.1 | -230.4916
0.5.0 | -230.4916
0.4.0 | -230.4916
0.2.1 | -230.77
apbs-smol-parallel.in | Parallel with 4 processors, 3 A sphere, focusing to 0.103 A, srfm smol | 1.4.1-binary | -229.3871 | -230.62
1.4 | -229.3871
1.3 | -229.3871
1.2.1 | -229.3871
1.2 | -229.38712
1.1.0 | -229.3872
1.0.0 | -229.3872
0.5.1 | -229.3872
0.5.0 | -229.3872
0.4.0 | -229.38721
0.3.2 | -226.3529
0.3.1 | -226.3529
0.3.0 | -229.5849
0.2.6 | -229.5849
0.2.5 | -229.5849
0.2.4 | -226.2276
0.2.3 | -226.2276
0.2.2 | -226.2276
0.2.0 | -226.228
0.1.8 | -226.23
apbs-smol-parallel.in | Finite Element Method, 3 A sphere, 3-level focusing to 0.188 A, srfm mol | 1.4.1-binary | -231.9550 | -230.62
apbs-smol-parallel.in | Finite Element Method, 3 A sphere, 3-level focusing to 0.188 A, srfm smol | 1.4.1-binary | -230.9760 | -230.62

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

4 The discrepancy in the result between versions 1.4 and 1.4.1-binary is most likely due to a reporting error.

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