Molecular Dynamics (MD) simulations offer a powerful computational approach for exploring the time-dependent behavior of molecular systems. Given your research focus on systems involving substances like toluene, water, graphene, and polymers like polystyrene and PMMA, MD can be incredibly useful.

Utilizing software packages like LAMMPS, GROMACS, and NAMD, researchers like you can simulate the dynamics of these molecular systems to investigate various properties and phenomena, such as wetting/dewetting, diffusion, and structural integrity.

Working primarily in a Linux environment, and leveraging the power of High-Performance Computing (HPC) clusters at IIT Delhi, allows for efficient parallel computations. This is especially vital when dealing with large or complex systems like decorated CNTs and graphene structures.

For better analysis and visualization, tools like VMD can be employed alongside Python libraries such as MDAnalysis and MDTraj. These tools provide deeper insights into the simulations, facilitating quality research that can be published in high-impact journals.

As you aim to expand your skill set, exploring other code repositories and software like moltemplate, plumed, and Materials Studio can offer new avenues for complex and accurate simulations. These tools can significantly broaden the horizons of your research work, potentially contributing to your goal of publishing a scientific research article by the end of this year.

Wetting and dewetting are critical phenomena observed at the interface between a liquid and a solid substrate. In the context of molecular dynamics, particularly with substances like toluene, water, or polymers like PMMA and polystyrene, these processes can have significant implications.

Wetting refers to the spreading of a liquid on a solid surface, governed by the intermolecular interactions between the liquid and solid molecules. The extent of wetting is often quantified by the contact angle—a low contact angle signifies good wetting, while a high angle indicates poor wetting or hydrophobicity.

On the other hand, dewetting is essentially the reverse of wetting; it is the spontaneous retraction of a liquid from a solid surface. The process of dewetting can occur due to changes in system parameters like temperature or concentration, or even due to external stimuli. The fundamental mechanism behind dewetting often involves breaking the favorable interactions between the liquid and the surface, which may be facilitated by a third phase or medium (for example, air in the case of aqueous systems).

These phenomena are vital in various applications, including coatings, lubrication, and even biological systems. For instance, a proper understanding of wetting and dewetting behaviors can be crucial for optimizing the interaction of water or toluene with materials like graphene or carbon nanotubes (CNTs) in your system. Sophisticated computational models, often employing molecular dynamics simulations through platforms like LAMMPS, GROMACS, or NAMD, offer powerful tools for understanding these complex interactions at the molecular level.