The example input files in this directory calculate the energy of placing an ion near a macromolecule.
This example was contributed by Dave Sept.
Input File | Description | APBS Version | Results (kJ/mol) | UHBD (kJ/mol) |
---|---|---|---|---|
apbs-mol-pdiel2.in | 0.53 A resolution, pdie 2, srfm mol | 1.3 | 15.59163 | 23.58 |
1.2.1 | 15.5819 | |||
1.2 | 15.5819 | |||
1.1.0 | 15.58192 | |||
1.0.0 | 15.5916 | |||
0.5.1 | 15.5916 | |||
0.5.0 | 15.5916 | |||
0.4.0 | 15.5916 | |||
apbs-smol-pdiel2.in | 0.53 A resolution, pdie 2, srfm smol | 1.3 | 23.55543 | 23.58 |
1.2.1 | 23.5458 | |||
1.2 | 23.5458 | |||
1.1.0 | 23.54582 | |||
1.0.0 | 23.5554 | |||
0.5.1 | 23.5554 | |||
0.5.0 | 23.5554 | |||
0.4.0 | 23.55541 | |||
0.3.2 | 21.4763 | |||
0.3.1 | 19.8794 | |||
0.3.0 | 19.8794 | |||
0.2.6 | 19.8794 | |||
0.2.5 | 19.8794 | |||
0.2.4 | 19.8794 | |||
0.2.3 | 19.8652 | |||
0.2.2 | 21.4530 | |||
0.2.1 | 21.453 | |||
0.2.0 | 21.453 | |||
0.1.8 | 21.45 | |||
apbs-mol-pdiel12.in | 0.53 A resolution, pdie 12, srfm mol | 1.3 | 18.02723 | 23.58 |
1.2.1 | 18.0176 | |||
1.2 | 18.0176 | |||
1.1.0 | 18.01762 | |||
1.0.0 | 18.0272 | |||
0.5.1 | 18.0272 | |||
0.5.0 | 18.0272 | |||
0.4.0 | 18.0272 | |||
apbs-smol-pdiel12.in | 0.53 A resolution, pdie 12, srfm smol | 1.3 | 19.28253 | 23.58 |
1.2.1 | 19.2728 | |||
1.2 | 19.2728 | |||
1.1.0 | 19.27282 | |||
1.0.0 | 19.2825 | |||
0.5.1 | 19.2825 | |||
0.5.0 | 19.2825 | |||
0.4.0 | 19.28251 | |||
0.3.2 | 21.4763 | |||
0.3.1 | 18.9205 | |||
0.3.0 | 17.4207 | |||
0.2.6 | 17.4207 | |||
0.2.5 | 17.4207 | |||
0.2.4 | 17.4207 | |||
0.2.3 | 17.4049 | |||
0.2.2 | 18.8953 | |||
0.2.1 | 18.895 | |||
0.2.0 | 18.895 | |||
0.1.8 | 18.90 |
1 The discrepancy in values between versions 0.4.0 and 0.3.2 is most likely due to three factors:
2 The discrepancy in values between versions 1.0.0 and 1.1.0 is due to a bugfix in the implementation of the boundary conditions. This bug introduces a very small error (generally less than 1%) the calculated results. This error is most prominent when the molecule substantially overlaps the boundary (e.g., in the current example) and is often symptomatic of insufficiently-large problem domains.
3 The discrepancy in values between versions 1.2.1 and 1.3 is most likely due to the following factor(s):
Please see the ChangeLog or the APBS documentation for more information.