The shell script ./runme 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 may need to edit the path to your Bourne-like shell in the ./runme script. You may also substitute any of the other APBS input files for apbs.in in the ./runme 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 | 0.4.0 | -229.77351 | -228.57 |
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 | 0.4.0 | -229.0123 | -228.57 |
apbs-mol-parallel.in | Parallel with 4 processors, 3 A sphere, focusing to 0.103 A, srfm mol | 0.4.0 | -230.4916 | -228.57 |
0.2.1 | -230.77 | |||
apbs-smol-parallel.in | Parallel with 4 processors, 3 A sphere, focusing to 0.103 A, srfm smol | 0.4.0 | -229.38721 | -228.57 |
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:
Please see the ChangeLog or the APBS documentation for more information.