Dear Subhadeep Sen

There are various resources available to help beginners learn how to run molecular dynamics (MD) simulations with GROMACS. Here are some of the top tutorials and resources:

GROMACS tutorials - GROMACS offers a variety of lessons on their website that cover a wide range of subjects, including protein-ligand binding, membrane proteins, and free energy calculations. These lessons are well-organized and offer step-by-step directions, input files, and thorough explanations of the theory behind each simulation.

YouTube Tutorials - Several YouTube channels provide GROMACS tutorials, including the GROMACS Tutorial Series by Justin Lemkul and the GROMACS Tutorials by Anirban Ghosh. These tutorials are excellent for novices since they provide a visual guidance to setting up and running simulations.

MD Simulations with GROMACS - Tsjerk Wassenaar's book provides a complete approach to doing MD simulations with GROMACS. It covers subjects such as system preparation, simulation setup, and data analysis, as well as practical examples and exercises to assist newcomers master the principles of MD simulations.

GROMACS User Forum - The GROMACS user forum is a great place for novices to ask questions and get advice from more experienced GROMACS users. The forum contains conversations on a wide range of topics, including simulation setup, troubleshooting, and data analysis.

GROMACS Online Course - GROMACS provides an online course that covers the fundamentals of MD simulations using GROMACS. The course comprises lectures, tutorials, and tests and is intended for novices with no prior expertise in MD simulations.

The above resources will provide a good starting point for anyone looking to learn the basics of MD simulations with GROMACS.

For beginners-

http://www.mdtutorials.com/gmx/

Best way is to refer the tutorial by Justin A. Lemkul, Ph.D

http://www.mdtutorials.com/gmx/

There are also certain others way with which simulation can be achieved which will come through experience in the field.