README for Actin-Dimer APBS examples

$Id: README.html 1266 2008-04-17 01:50:01Z sobolevnrm $

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 1.0.0 104.868 106.7
(1.00 A res., NPBE)
0.5.1 104.8683
0.5.0 105.03382
0.4.0 104.8895
apbs-smol-auto.in Sequential, 2-level focusing to ≤ 0.725 A, NPBE, srfm smol 1.0.0 109.5841 106.7
(1.00 A res., NPBE)
0.5.1 109.58413
0.5.0 109.75182
0.4.0 109.60431
0.3.2 90.8704
0.3.1 88.6101
0.3.0 88.6101
0.2.6 88.6101
0.2.5 88.6101
0.2.4 88.6101
0.2.3 88.6064
0.2.2 90.829
0.2.1 90.829
0.2.0 90.829
0.1.8 90.84
apbs-mol-parallel.in Parallel with 8 processors, focusing to ~0.9 A, LPBE, srfm mol 1.0.0 98.16434 106.7
(1.00 A res., NPBE)
0.5.198.16543
0.5.098.35302
0.4.098.1834
apbs-smol-parallel.in Parallel with 8 processors, focusing to ~0.9 A, LPBE, srfm smol 1.0.0 115.55734 106.7
(1.00 A res., NPBE)
0.5.1115.55843
0.5.0115.74922
0.4.0115.57511
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:

2 The discrepancy in values between versions 0.5.0 and 0.4.0 is most likely due to the following factor(s):

3 The discrepancy in values between versions 0.5.1 and 0.5.0 is most likely due to the following factor(s):

4 The discrepancy in values between versions 0.5.1 and 1.0.0 was due to the execution of the previous APBS tests on a PowerPC platform with the XLC/XLF compilers. Running with binaries compiled with gcc/gfortran or the Intel compilers gives identical results between versions 0.5.1 and 1.0.0.

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