README for ion-protein APBS examples

$Id: README.html 1440 2009-11-17 20:37:08Z yhuang01 $

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 1.2.1 15.5819 23.58
1.215.5819
1.1.015.58192
1.0.015.5916
0.5.115.5916
0.5.015.5916
0.4.015.5916
apbs-smol-pdiel2.in 0.53 A resolution, pdie 2, srfm smol 1.2.1 23.5458 23.58
1.223.5458
1.1.023.54582
1.0.023.5554
0.5.123.5554
0.5.023.5554
0.4.023.55541
0.3.221.4763
0.3.119.8794
0.3.019.8794
0.2.619.8794
0.2.519.8794
0.2.419.8794
0.2.319.8652
0.2.221.4530
0.2.121.453
0.2.021.453
0.1.821.45
apbs-mol-pdiel12.in 0.53 A resolution, pdie 12, srfm mol 1.2.1 18.0176 23.58
1.218.0176
1.1.018.01762
1.0.018.0272
0.5.118.0272
0.5.018.0272
0.4.018.0272
apbs-smol-pdiel12.in 0.53 A resolution, pdie 12, srfm smol 1.2.1 19.2728 23.58
1.219.2728
1.1.019.27282
1.0.019.2825
0.5.119.2825
0.5.019.2825
0.4.019.28251
0.3.221.4763
0.3.118.9205
0.3.017.4207
0.2.617.4207
0.2.517.4207
0.2.417.4207
0.2.317.4049
0.2.218.8953
0.2.118.895
0.2.018.895
0.1.818.90

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.

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