# 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 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 | 1.4.1-binary | 104.8683 | 106.7 (1.00 A res., NPBE)
1.4 | 104.8683
1.3 | 104.86838
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 | 1.4.1-binary | 109.5841 | 106.7 (1.00 A res., NPBE)
1.4 | 109.5841
1.3 | 109.58418
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 | 1.4.1-binary | 98.1746 | 106.7 (1.00 A res., NPBE)
1.4 | 98.1746
1.3 | 98.17468
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 | 1.4.1-binary | 115.5421 | 106.7 (1.00 A res., NPBE)
1.4 | 115.54219
1.3 | 115.54228
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:

- A bug fix in Vacc_molAcc which removed spurious regions of high internal dielectric values
- A switch in the algorithm used to compute the dielectric smoothing for srfm smol.
- The addition of the Vacc sphere density (sdens keyword) as a variable and a change in the default sdens value from 3.0 to 10.0

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

- A change in the autofocusing routine for APBS

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

- Bug fix regarding multipole behavior for neutral proteins

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):

- Fixed a bug in Vpmg_fillcoCoefMolIon which causes npbe based calculations to return very large energies

8 The discrepancy in values between versions 1.2.1 and 1.3 is most likely due to the following factor(s):

- Fixed a bug in Vpmg.c which causes zero potential values on boundaries in non-focusing calculations.

9 The discrepancy in values between versions 1.3 and 1.4 is most likely due to the following factor(s):

- Translation of contrib/pmgZ library from FORTRAN to C
- Differences in numerical implementations between FORTRAN and C compilers result in small round-off discrepencies
- Small margins due to these round-off discrepencies acumulate in the computations

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