Molecular Dynamics Simulation with GROMACS: A Beginner's Tutorial

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.
Participate in the workshop: https://bit.ly/41TytXj

To get the simulation parameter files click on this link: https://bit.ly/3LVCTrc


Outlines

00:14 Introduction
00:56 How to find protein structures
03:24 Introducing the PDB file format
05:07 Visualise a protein structure using VMD
05:46 Remove water molecules from the structure
07:43 Explaining the GROMACS input flowchart
11:37 Fixing missing atoms in PDB files
13:22 Create a topology file for a protein structure
15:24 Explaining the GROMACS coordinate file (gro)
16:13 Explaining the GROMACS topology file
19:37 Remove GROMACS backup files
20:06 Setting up a PBC box
23:11 Adding solvent molecules to the simulation box
25:00 Adding ions
28:43 Minimising system
34:10 Equilibrating system in the NVT ensemble
36:01 Explaining position restraints in GROMACS
38:28 Explaining the GROMACS MDP file
45:01 How to check if the system reached equilibrium
47:09 Equilibrating system in the NPT ensemble
51:59 Performing the product simulation
52:49 Explaining GROMACS compressed and uncompressed trajectory files
55:05 Explaining GROMACS output files
56:14 How to restart and extend a simulation
01:00:35 Visualise and check trajectory files using VMD
01:03:19 Performing basic analysis of simulation results
01:04:44 RMSD analysis
01:07:12 Radius of gyration analysis

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