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Sample calculation using the protein attach-pull-release (APR)\u00a0method on the BZT-7 ligand to the BRD4 first bromodomain, with\u00a0the 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\u00a0sample calculation. To obtain\u00a0the binding free energies from the simulations using MBAR, instructions can be found in the ./Base-SPC/analysis/get-results.bash script.\u00a0
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