This article provides introductory tutorials for performing molecular dynamics (MD) simulations of proteins using the GROMACS package. Three exercises are detailed: simulating a single protein, setting up a protein complex, and performing umbrella sampling simulations to model the unfolding of a short polypeptide. The tutorials illustrate essential features and input settings, aiming to provide new users with a general understanding of foundational workflows for MD simulations. Molecular dynamics simulations allow investigation of systems with high spatial and temporal resolution. The accuracy of MD simulations depends on the quality of the force field, the energy equation, and sampling adequacy. Classical force fields apply Newtonian mechanics to compute atomic energies and forces. Sampling methods include long unbiased simulations and enhanced sampling techniques with external biasing potentials. Several software packages, including GROMACS, are used for MD simulations. GROMACS is highlighted for its features, force field compatibility, and performance for large systems. The tutorials focus on GROMACS for simulating polypeptides and proteins. The exercises use the CHARMM36 force field, which is external to GROMACS. The CHARMM36m force field is used for proteins in aqueous environments. The tutorials include steps for preparing protein topologies, defining unit cells, adding solvent and ions, and performing energy minimization, equilibration, and MD simulations. Key steps include using pdb2gmx to generate protein topologies, editconf to define unit cells, solvate to add solvent, and genion to add ions. Energy minimization, equilibration under NVT and NPT ensembles, and production MD simulations are performed. Analysis tools like rms, rmsf, hbond, and dssp are used to analyze structural and dynamic properties. The tutorials also cover principal component analysis (PCA) for identifying low-frequency motions in biomolecules. The analysis includes free energy surfaces and eigenvalues for eigenvectors. The exercises demonstrate the preparation of simulation systems, equilibration, and analysis of MD trajectories. The article emphasizes the importance of planning analysis before simulations and highlights the flexibility of GROMACS for various biomolecular simulations. It also notes that convergence and replicate simulations are critical but beyond the scope of the tutorial. The workflow provides a starting point for learning GROMACS and performing simulations of single biomolecules in water.This article provides introductory tutorials for performing molecular dynamics (MD) simulations of proteins using the GROMACS package. Three exercises are detailed: simulating a single protein, setting up a protein complex, and performing umbrella sampling simulations to model the unfolding of a short polypeptide. The tutorials illustrate essential features and input settings, aiming to provide new users with a general understanding of foundational workflows for MD simulations. Molecular dynamics simulations allow investigation of systems with high spatial and temporal resolution. The accuracy of MD simulations depends on the quality of the force field, the energy equation, and sampling adequacy. Classical force fields apply Newtonian mechanics to compute atomic energies and forces. Sampling methods include long unbiased simulations and enhanced sampling techniques with external biasing potentials. Several software packages, including GROMACS, are used for MD simulations. GROMACS is highlighted for its features, force field compatibility, and performance for large systems. The tutorials focus on GROMACS for simulating polypeptides and proteins. The exercises use the CHARMM36 force field, which is external to GROMACS. The CHARMM36m force field is used for proteins in aqueous environments. The tutorials include steps for preparing protein topologies, defining unit cells, adding solvent and ions, and performing energy minimization, equilibration, and MD simulations. Key steps include using pdb2gmx to generate protein topologies, editconf to define unit cells, solvate to add solvent, and genion to add ions. Energy minimization, equilibration under NVT and NPT ensembles, and production MD simulations are performed. Analysis tools like rms, rmsf, hbond, and dssp are used to analyze structural and dynamic properties. The tutorials also cover principal component analysis (PCA) for identifying low-frequency motions in biomolecules. The analysis includes free energy surfaces and eigenvalues for eigenvectors. The exercises demonstrate the preparation of simulation systems, equilibration, and analysis of MD trajectories. The article emphasizes the importance of planning analysis before simulations and highlights the flexibility of GROMACS for various biomolecular simulations. It also notes that convergence and replicate simulations are critical but beyond the scope of the tutorial. The workflow provides a starting point for learning GROMACS and performing simulations of single biomolecules in water.