Molecular Dynamics Simulation (MDS) Full Tutorial Using GROMACS | Beginner to Analysis | WSL2 Linux

In this video, I walk you through a complete Molecular Dynamics Simulation (MDS) pipeline using GROMACS 2023.2 on WSL2/Linux from scratch — starting from a raw PDB file all the way to trajectory analysis and PyMOL visualization. 🔬 What's Covered: ✅ What is Molecular Dynamics Simulation ✅ Use cases in drug discovery & cancer research ✅ WSL2 + GROMACS installation ✅ Protein structure preparation (PDB: 1UBQ Ubiquitin) ✅ Topology generation — OPLS-AA/L force field ✅ Solvation — SPC/E water box ✅ Ionization — 0.15M NaCl physiological salt ✅ Energy Minimization ✅ NVT & NPT Equilibration ✅ Production MD — 1ns trajectory ✅ RMSD | RMSF | H-bond | SASA | Radius of Gyration ✅ PyMOL trajectory visualization ⚙️ Tools Used: GROMACS 2023.2 | WSL2 | Ubuntu | PyMOL | OPLS-AA/L 📌 PDB Used: 1UBQ (Ubiquitin) If you're a Biotechnology, Bioinformatics or Computational Biology student looking to get hands-on with MDS — this is your complete beginner-friendly guide. 🔔 Subscribe for more computational biology tutorials. ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ #MolecularDynamics #GROMACS #Bioinformatics #MDS #ComputationalBiology #Biotechnology #DrugDiscovery #StructuralBiology #Ubiquitin #WSL2 #PyMOL #Linux #ProteinSimulation #RMSD #RMSF #SASA #MDSimulation #BioinformaticsTutorial #GROMACS2023 #CancerResearch ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━