• -f, -force_warning: By default, missing statistics for any anchors will generate fatal errors. This option will instead raise a warning and attempt the calculation anyway. • -n NUM_ERROR_SAMPLES: This argument specifies the number of error samples to generate for estimating the error/uncertainty of computed values. The default value is 100. • -S STRIDE_ERROR_SAMPLES: This argument specifies the number of strides between saved error samples. An argument of None automatically assigns the quantity at the number of milestones in the model squared. The default value is None. • -K SKIP_ERROR_SAMPLES, -skip_error_samples SKIP_ERROR_SAMPLES: This argument specifies the number of error samples to skip before using them. An argument of None automatically assigns the quantity at ten times the number of milestones in the model squared. The default value is None. • -d IMAGE_DIRECTORY: By 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. • -s, -skip_checks: By default, post-simulation checks will be run before the analysis is started, and if the checks fail, the analysis will not proceed. This argument bypasses those checks and allows the analysis to proceed anyways. • -t MINIMUM_TIME: A user may wish to skip a simulation time for each anchor before counting the transitions for milestoning analysis. When performing analysis, we enter the time (in ps) to skip a portion of the production simulations.