As mentioned previously, the HIDR program requires a model.xml file to run the SMD simulations, so we run the prepare.py script on a model input file. It should be noted that the <md_steps_per_anchor> tag defines the number of MD simulation steps per anchor, and for tutorial purposes, the simulation steps in each anchor are reduced. The <root_directory> tag has to be explicitly defined by the user in the input_SMD_HIDR.xml file. To run the prepare.py script on the model input file, we execute the following command in the terminal: