# README for ion-protein APBS examples

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 | 1.4.1-binary | 15.5916 | 23.58
1.4 | 15.5916
1.3 | 15.59163
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 | 1.4.1-binary | 23.5554 | 23.58
1.4 | 23.5554
1.3 | 23.55543
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 | 1.4.1-binary | 18.0272 | 23.58
1.4 | 18.0272
1.3 | 18.02723
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 | 1.4.1-binary | 19.2825 | 23.58
1.4 | 19.2825
1.3 | 19.28253
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:

- 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

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):

- Fixed a bug in Vpmg.c which causes zero potential values on boundaries in non-focusing calculations.

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