README for Born APBS examples

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

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.

The shell script ./runme.sh will generate ions of several radii and calculate the solvation energies (which will appear in OUTPUT-XXX, where XXX is the particular radius of interest). Please see apbs.in for details on the particular solvation energy calculations. Analytical results are given in pmf.dat. Note: You will need to ensure that the 'apbs' binary is in your path prior to running ./runme.sh. You may also need to edit the path to your Bourne-like shell in the ./runme.sh script.

This example was contributed by Nathan Baker.

Input FileDescriptionAPBS VersionResults (kJ/mol)Analytical (kJ/mol)
apbs-mol-auto.in Sequential, 3 A sphere, 3-level focusing to 0.188 A, srfm mol 1.2.1 -229.7735 -228.57
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 1.2.1 -229.0124 -228.57
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 1.2.1 -230.4918 -228.57
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 1.2.1 -229.3871 -228.57
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

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.