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 File | Description | APBS Version | Results (kJ/mol) | UHBD (kJ/mol) |
---|---|---|---|---|
apbs-mol-auto.in | Sequential, 2-level focusing to ≤ 0.725 A, NPBE, srfm mol | 1.3 | 104.86838 | 106.7 (1.00 A res., NPBE) |
1.2.1 | 104.867 | |||
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 | 1.3 | 109.58418 | 106.7 (1.00 A res., NPBE) |
1.2.1 | 109.5829 | |||
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 | 1.3 | 98.17468 | 106.7 (1.00 A res., NPBE) |
1.2.1 | 98.17337 | |||
1.2 | 98.16356 | |||
1.1.0 | 98.16305 | |||
1.0.0 | 98.16434 | |||
0.5.1 | 98.16543 | |||
0.5.0 | 98.35302 | |||
0.4.0 | 98.1834 | |||
apbs-smol-parallel.in | Parallel with 8 processors, focusing to ~0.9 A, LPBE, srfm smol | 1.3 | 115.54228 | 106.7 (1.00 A res., NPBE) |
1.2.1 | 115.54097 | |||
1.2 | 115.55636 | |||
1.1.0 | 115.55605 | |||
1.0.0 | 115.55734 | |||
0.5.1 | 115.55843 | |||
0.5.0 | 115.74922 | |||
0.4.0 | 115.57511 | |||
0.3.2 | 87.1121 | |||
0.3.1 | 87.1121 | |||
0.3.0 | 90.2573 | |||
0.2.6 | 90.2573 | |||
0.2.5 | 90.2573 | |||
0.2.4 | 90.2573 | |||
0.2.3 | 90.2543 | |||
0.2.2 | 91.9450 | |||
0.2.1 | 91.945 | |||
0.2.0 | 91.939 | |||
0.1.8 | 91.67 |
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.
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):
8 The discrepancy in values between versions 1.2.1 and 1.3 is most likely due to the following factor(s):
Please see the ChangeLog or the APBS documentation for more information.