This directory serves as the root directory for the APBS test suite. In each directory you will find example input files to use with APBS and a README file displaying the results for different versions of APBS.

Executing make test in each directory will run the examples for that directory and log the results to TESTRESULTS.log. Executing make test from the root examples directory will run all the tests listed below. Tests will either pass, pass with rounding error (within 10^-9 of the expected result), or fail outright.

Example	README file	Source	Description
Actin dimer (actin-dimer)	actin-dimer/README.md	Dave Sept	Calculate binding energies for actin dimers. This is an example of a large biomolecule binding energy calculation that often requires parallel focusing.
Alkane nonpolar solvation energies (alkanes)	alkanes/README.md	Nathan Baker, Jason Wagoner	Calculate nonpolar solvation energies for various alkanes. Taken from Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006.
Born ion (born)	born/README.md	Nathan Baker	Calculate solvation energies for ions of various sizes and compare to the analytical results.
FKBP (FKBP)	FKBP/README.md	Jung-Hsin Lin	Binding of various (small) ligands to FKBP. Analogous to HCA binding case (except it works).
HCA ligand binding (hca-bind)	hca-bind/README.md	UHBD	Calculate the binding of a small molecule (acetazolamide) to a medium-sized protein (human carbonic anhydrase).
Acetic acid ionization (ionize)	ionize/README.md	UHBD	Calculate electrostatic contributions to the ionization energy of acetic acid.
Ion-ion PMF (ion-pmf)	ion-pmf/README.md	Nathan Baker	Calculate solvation energies and solvation force components for ion pairs.
Ion-protein interaction energies (ion-protein)	ion-protein/README.md	Dave Sept	Calculate polar energy of placing an ion near a macromolecule.
PKA-balanol binding (pka-lig)	pka-lig/README.md	Chung Wong	Calculate binding energies of a ligand to protein kinase A.
Coulomb's law (point-pmf)	point-pmf/README.md	Nathan Baker	See how well we do reproducing Coulomb's law.
Methanol solvation (solv)	solv/README.md	UHBD	Calculate the solvation energies of methanol and methoxide.
Protein-RNA interactions (protein-rna)	protein-rna/README.md	David Draper	Calculate the salt dependence of protein interactions with box B RNA hairpin.
Geometric flow solvation model	geoflow/README.md	Elizabeth Jurrus	Calculate the dielectric interface profile across the solute-solvent boundary in a thermodynamically sef-consistent fashion.