# Summary This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI). Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb\_conda_kernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml file. # Parameters ## Inputs Parameters needed to configure the workflow: * **pdbCode**: PDB code of the protein-ligand complex structure (e.g. 1AKI) ## Outputs Output files generated (named according to the input parameters given above): * **output\_md\_gro**: final structure of the MD setup protocol * **output\_md\_trr**: final trajectory of the MD setup protocol * **output\_md\_cpt**: final checkpoint file * **output\_gppmd\_tpr**: final tpr file * **output\_genion\_top\_zip**: final topology of the MD system