<p>Sample calculation using the protein attach-pull-release (APR) method on the BZT-7 ligand to the BRD4 first bromodomain, with the SPC/E water model. Instructions for the automatic creation of the system are included in the automated.bash script in the ./Base-SPC/ folder, and the ./BZT-7-SPC/ folder contains the sample calculation. To obtain the binding free energies from the simulations using MBAR, instructions can be found in the ./Base-SPC/analysis/get-results.bash script. </p