This article provides a comprehensive guide to performing atomistic molecular dynamics (MD) simulations of proteins using the open-source software GROMACS. It includes three detailed tutorials: simulating a single protein, setting up a protein complex, and performing umbrella sampling to model the unfolding of a short polypeptide. The tutorials cover essential features and input settings, aiming to provide new users with a general understanding of foundational workflows. The background section explains the principles of MD simulations, emphasizing the importance of force fields, sampling methods, and software packages like GROMACS. It also discusses the CHARMM36 force field, which is used in the tutorials, and its installation and proper use. The prerequisites and installation section outlines the requirements for using GROMACS, including the need for version 2024.1 and the CHARMM36 force field. It provides installation instructions and notes on file types and command-line conventions. The exercises section details the steps for each tutorial, including preparing protein topology, defining periodic cells, adding solvents and ions, performing energy minimization, equilibration, and unbiased MD simulations. It also covers analyzing simulation outcomes using tools like trjconv, rmsf, hbond, dssp, and principal component analysis (PCA). The article concludes with a discussion on the general method and key concepts, emphasizing the importance of planning analysis based on scientific questions and the flexibility of the provided workflow.This article provides a comprehensive guide to performing atomistic molecular dynamics (MD) simulations of proteins using the open-source software GROMACS. It includes three detailed tutorials: simulating a single protein, setting up a protein complex, and performing umbrella sampling to model the unfolding of a short polypeptide. The tutorials cover essential features and input settings, aiming to provide new users with a general understanding of foundational workflows. The background section explains the principles of MD simulations, emphasizing the importance of force fields, sampling methods, and software packages like GROMACS. It also discusses the CHARMM36 force field, which is used in the tutorials, and its installation and proper use. The prerequisites and installation section outlines the requirements for using GROMACS, including the need for version 2024.1 and the CHARMM36 force field. It provides installation instructions and notes on file types and command-line conventions. The exercises section details the steps for each tutorial, including preparing protein topology, defining periodic cells, adding solvents and ions, performing energy minimization, equilibration, and unbiased MD simulations. It also covers analyzing simulation outcomes using tools like trjconv, rmsf, hbond, dssp, and principal component analysis (PCA). The article concludes with a discussion on the general method and key concepts, emphasizing the importance of planning analysis based on scientific questions and the flexibility of the provided workflow.