A molecular graph is a 2D representation of a molecule where atoms and bonds are typically simplified as vertices and edges of the graph, respectively. Graphs can be represented in matrix form, leading to computationally efficient methods to extract information from the system. In this work, we resort to the adjacency matrix, which contains topological information, i.e., the covalent and non-covalent bonds within the atoms. The knowledge of this matrix at each snapshot ultimately provides us with the required information about the isolated molecular clusters present during the simulation.