README for Actin-Dimer APBS examples


The example input files in this directory calculate binding energies for actin dimers. This is an example of a large biomolecule binding energy calculation that often requires parallel focusing.

This example was contributed by Dave Sept.

Input FileDescriptionAPBS VersionResults (kJ/mol)UHBD (kJ/mol)
apbs-mol-auto.in Sequential, 2-level focusing to <=0.725 A, NPBE, srfm mol 0.4.0104.8895 106.7
(1.00 A res., NPBE)
apbs-smol-auto.in Sequential, 2-level focusing to <=0.725 A, NPBE, srfm smol 0.4.0109.60431 106.7
(1.00 A res., NPBE)
0.3.290.8704
0.3.188.6101
0.3.088.6101
0.2.688.6101
0.2.588.6101
0.2.488.6101
0.2.388.6064
0.2.290.829
0.2.190.829
0.2.090.829
0.1.890.84
apbs-mol-parallel.in Parallel with 8 processors, focusing to ~0.9 A, LPBE, srfm mol 0.4.098.1834 106.7
(1.00 A res., NPBE)
apbs-smol-parallel.in Parallel with 8 processors, focusing to ~0.9 A, LPBE, srfm smol 0.4.0115.57511 106.7
(1.00 A res., NPBE)
0.3.287.1121
0.3.187.1121
0.3.090.2573
0.2.690.2573
0.2.590.2573
0.2.490.2573
0.2.390.2543
0.2.291.9450
0.2.191.945
0.2.091.939
0.1.891.67

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.