These programs (wham and wham-2d) implement the Weighted Histogram Analysis Method of Kumar, et al ("Multidimensional free-energy calculations using the weighted histogram analysis method", J. Comput. Chem., 16:1339-1350, 1995). The code generally follows the notation used by Benoit Roux ("The calculation of the potential of mean force using computer simulations", Comput. Phys. Comm., 91:275-282, 1995). Consult these papers for the theoretical background and justification for the method.
This program was initially released in 2000, when I was a postdoc in Jay Ponder's group, but I only migrated it to GitHub in 2026.
If you use this code as part of an original piece of research, I'd appreciate a reference or acknowledgment. There's no publication to reference, so please use something like:
Grossfield, A, "WHAM: an implementation of the weighted histogram analysis method", https://github.com/agrossfield/wham, version XXXX
For that matter, just letting me know what you're using my code for would be nice, although again I don't insist upon it.