GROMACS in 60 Minutes: Learn Protein-Water Simulation Fast!

Accelerate your molecular dynamics journey with this 60-minute crash course on protein-water simulation using GROMACS. Learn how to prepare your system, solvate proteins, add ions, and run energy minimization and MD simulations. This step-by-step tutorial is perfect for beginners and researchers looking to build a strong foundation in computational biology and bioinformatics. Want to simulate a protein in water using GROMACS but don’t know where to start? In this beginner-friendly, step-by-step tutorial, you'll learn how to set up and run a complete protein-water molecular dynamics (MD) simulation in just 60 minutes! 🧪 What you’ll learn: How to prepare your protein structure Solvating the protein in a water box Adding ions for neutralization Energy minimization Equilibration and production MD run Basic trajectory analysis This video is perfect for students, researchers, and beginners in bioinformatics, structural biology, or computational chemistry. 📌 No prior GROMACS experience required! Protein simulation using Gromacs (solvation model) PDB ID: https://www.rcsb.org/structure/6LU7 CHARMM Forecefield: http://mackerell.umaryland.edu/charmm... CHARMMGUI: https://www.charmm-gui.org GROMACS Tutorial: http://www.mdtutorials.com/gmx/lysozy... MDP files: ions.mdp : http://www.mdtutorials.com/gmx/lysozy... minim.mdp: http://www.mdtutorials.com/gmx/lysozy... nvt.mdp: http://www.mdtutorials.com/gmx/lysozy... npt.mdp: http://www.mdtutorials.com/gmx/lysozy... md.mdp: http://www.mdtutorials.com/gmx/lysozy... Commands: gmx pdb2gmx -f step1_pdbreader.pdb -o protein_processed.gro -water spce gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt cubic gmx solvate -cp protein_newbox.gro -cs spc216.gro -o proein_solv.gro -p topol.top gmx grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr gmx genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA -nname CL -neutral gmx grompp -f minim.mdp -c protein_solv_ions.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr gmx mdrun -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr gmx mdrun -v -deffnm npt gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md.tpr gmx mdrun -v -deffnm md Github for MD simulation: https://github.com/pritampanda15/Mole... GROMACS Manual: https://manual.gromacs.org/current/re... #GROMACS #ProteinWaterSimulation #MolecularDynamics #Bioinformatics #ComputationalBiology #GROMACSTutorial #ProteinSimulation #MDSimulation #WaterSolvation #StructuralBiology 🔔 Don’t forget to like, comment, and subscribe for more tutorials on GROMACS, molecular dynamics, and bioinformatics tools. ================================================================== Welcome to Omixium! This channel is dedicated to empowering the next generation of scientists with hands-on tutorials, deep dives, and tool walkthroughs in: 🔬 Bioinformatics & Computational Biology 🧠 AI in Drug Discovery & Protein Design ⚗️ Molecular Docking, MD Simulations & Systems Biology 🧬 Single-cell RNA-seq, Multi-omics & NGS Pipelines 👨‍💻 AI Coding for Biology (Claude, Gemini, GPT) 🧪 New videos every week — for scientists, students, coders, and curious minds! --- 🌐 Stay Connected: 🔗 LinkedIn: [Pritam Kumar Panda](  / pritam-kumar-panda  ) 🌍 Website: [https://www.atomodyssey.com](https://www.atomodyssey.com) 📧 Contact: [[email protected]](mailto:[email protected]) 💻 GitHub: [https://github.com/pritampanda15](https://github.com/pritampanda15)