This directory (and its subdirectories) provides the input files for running and analyzing the simulations reported in the paper "Sampling conformational changes of bound ligands using Nonequilibrium Candidate Monte Carlo".

• ligand1: directory containing input files for running simulations with ligand 1.
• ligand2: directory containing input files for running simulations with ligand 2.
• ligand3: directory containing input files for running simulations with ligand 3.
• ligand4: directory containing input files for running simulations with ligand 4.
• plots_paper: directory containing matlab scripts used to generate plots for the paper. The name of the scripts contain the figure number it was used for.
• scripts: directory containing scripts and Amber input files used to run and post-process MD and MD/NCMC simulations.
• blues-master.tgz: BLUES code used for running MD/NCMC simulations.