Скачать или смотреть 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

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