The common MD engines run at commandline.However, there are some GUI based things out there. Free of charge is i.e. VMDs QwikMD plugin that runs with NAMD. On the commercial side, there is for example Molecular Operating Environment (MOE) and Maestro (Schrodinger) but they are expensive.

There are some step-by-step tutorials on GitHub. Just search for Lammps tutorial. And it's relatively easy to run Lammps by jupyter notebook but you still need to learn about commandline.

Usually, I run MD simulations on terminal using LAMMPS. What exactly you are trying to simulate? I might be able to help you.

Ziye Deng thank you for your answer! Would you be so kind to share several links with me in order to make sure that we are talking about the same thing?

Yours sincerely,

M. Sc. Vadym Chibrikov

Department of Microstructure and Mechanics of Biomaterials

Institute of Agrophysics, Polish Academy of Sciences

Gaurav Arora thank you for your answer! I am just trying to learn some basic things on that theme. Would you be so kind to share some sort of materials with me?

Yours sincerely,

M. Sc. Vadym Chibrikov

Department of Microstructure and Mechanics of Biomaterials

Institute of Agrophysics, Polish Academy of Sciences

I hope that it will provide you with some basics regarding LAMMPS-based MD simulations [ https://lammpstutorials.github.io/ ]. Furthermore, there are some other directories available for the same. For carbon nanostructures, you can refer to the following papers:

Article Topological defects embedded large-sized single-walled carbo...

Article Unraveling the influence of grain boundaries on the mechanic...

Article Electromechanical response of stacked h-BN layers: A computa...

Article Investigation of hydrogen adsorption behavior of graphene un...

Article Transversely isotropic elastic properties of multi-walled bo...

https://github.com/mrkllntschpp/lammps-tutorials

I hope it is helpful