This step-by-step tutorial is designed for beginners who want to learn how to set up and run molecular dynamics (MD) simulations using GROMACS. This video will not just show the process; I will explain each step and the reasons behind it. Furthermore, I will discuss GROMACS’s input and output files. This video is part of the Online GROMACS Workshop hosted by InsilicoSci.
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Outlines
Introduction
How to find protein structures
Introducing the PDB file format
Visualise a protein structure using VMD
Remove water molecules from the structure
Explaining the GROMACS input flowchart
Fixing missing atoms in PDB files
Create a topology file for a protein structure
Explaining the GROMACS coordinate file (gro)
Explaining the GROMACS topology file
Remove GROMACS backup files
Setting up a PBC box
Adding solvent molecules to the simulation box
Adding ions
Minimising system
Equilibrating system in the NVT ensemble
Explaining position restraints in GROMACS
Explaining the GROMACS MDP file
How to check if the system reached equilibrium
Equilibrating system in the NPT ensemble
Performing the product simulation
Explaining GROMACS compressed and uncompressed trajectory files
Explaining GROMACS output files
How to restart and extend a simulation
Visualise and check trajectory files using VMD
Performing basic analysis of simulation results
RMSD analysis
Radius of gyration analysis
Downloads
To get the GROMACS simulation parameters files, click the button below. This is a compressed tar.gz file. You can extract files using the following command.
tar -xvzf MD_Simulation_with_GROMACS_A_Beginner’s_Tutorial.tgz
This video is part of the Online GROMACS Workshop hosted by InsilicoSci. To check the complete workshop, click here.