python ∼/seekr2/seekr2/prepare.py \ input_SMD_HIDR.xml The path to the model.xml file is frequently used as an argument in many subsequent SEEKR2 processes, especially during the run phase. It is to be noted that directly altering the model.xml without reinitiating prepare.py is not recommended. The run.py script initiates the run phase, and the following command launches the script to run MD simulations within the SEEKR2 milestones.