Dive into the second session of a Gromacs beginner tutorial on Molecular Dynamics Simulations. Learn essential MD simulation steps, including system solvation, neutralization, energy minimization, and equilibration. Explore how to generate and interpret RMSD and RMSF graphs in Windows. Access provided .mdp files for ions, minimization, NVT, NPT, and MD simulations to enhance your practical understanding. Follow along with step-by-step instructions on using mdrun, analyzing potential energy, and performing equilibration with grompp. Gain valuable insights into bioinformatics and computational chemistry techniques for studying molecular systems.