In this work we consider an application of physically-inspired sociodynamical model to the modelling of the evolution of email-based social network. In contrary to the standard approach of sociodynamics, which assumes expressing of system dynamics with heuristically-defined simple rules, we postulate the inference of these rules from the real data and their application within a dynamic molecular model. We present how to embed the n-dimensional social space in Euclidean one. Then, inspired by the LennardJones potential, we define a data-driven social potential function and apply the resultant force to a real e-mail communication network in a course of a molecular simulation, with network nodes taking on the role of interacting particles. We discuss all steps of the modelling process, from data preparation, through embedding and the molecular simulation itself, to transformation from the embedding space back to a graph structure. The conclusions, drawn from examining the resultant networks in stable, minimum-energy states, emphasize the role of the embedding process projecting the non-metric social graph into the Euclidean space, the significance of the unavoidable loss of information connected with this procedure and the resultant preservation of global rather than local properties of the initial network. We also argue applicabil- ity of our method to some classes of problems, while also signalling the areas which require further research in order to expand this applicability domain.