# README for Born APBS examples

$Id: README.html 1264 2008-04-16 16:41:31Z 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 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 | 1.0.0 | -229.7735 | -228.57
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 | 1.0.0 | -229.0123 | -228.57
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 | 1.0.0 | -230.4916 | -228.57
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 | 1.0.0 | -229.3872 | -228.57
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:

- 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

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