README for Actin-Dimer APBS examples

$Id: README.html 1441 2009-11-18 03:04:14Z yhuang01 $

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 1.2.1 104.867 106.7
(1.00 A res., NPBE)
1.2 104.867
1.1.0 104.8675
1.0.0 104.868
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 1.2.1 109.5829 106.7
(1.00 A res., NPBE)
1.2 109.5829
1.1.0 109.58295
1.0.0 109.5841
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 1.2.1 98.17337 106.7
(1.00 A res., NPBE)
1.298.16356
1.1.098.16305
1.0.098.16434
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 1.2.1 115.54097 106.7
(1.00 A res., NPBE)
1.2115.55636
1.1.0115.55605
1.0.0115.55734
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.

5 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.

6 APBS 1.2 has switched the multigrid smoothing algorithm from standard Gauss-Seidel to Gauss-Seidel red/black in order to facilitate parallelization. This switch has caused small differences in individual calculation energies which, when combined to the final answer, create larger errors (up to 0.04%). These errors can be reduced by resetting the APBS error tolerance to 1e-9 or smaller values. For a more detailed explanation, please see here.

7 The discrepancy in values between versions 1.2 and 1.2.1 is most likely due to the following factor(s):

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