• -s K_ON_STATE: This argument allows us to define the bound state used to compute the kon value. If we want to specify a particular bound state, we include the -s option followed by the state name. • -d IMAGE_DIRECTORY: Using this argument, we can define the directory where plots and images will be saved. If we want to specify a different directory, we include the -d option followed by the desired directory path. By default, all the plots will be saved to the images_and_plots directory. • -c CUTOFF: This argument sets the minimum convergence value required to conclude that the calculations have converged for a given anchor. The default value is 0.1, but we can specify a different cutoff value by including the -c option followed by the desired value. • -m MINIMUM_ANCHOR_TRANSITIONS: Using this argument, we can set the minimum number of transitions that must be observed per milestone in a given anchor as a criterion for SEEKR2 simulations. The default value is 100, but we can specify a different value by including the -m option followed by the desired number. • -l, -long_converge: This argument determines whether to run a complete convergence analysis.