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.
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 website for more information.