Physics Models and Machine Learning in Molecular Dynamics

Abstract

Abstract. Tackling the complexity of particle interactions, this investigation introduces a unified computational methodology employing Moldy, Gnuplot, and Visual Molecular Dynamics (VMD). Inspired by the n-body problem's persistent intrigue, specifically the three-body dynamics within molecular systems, we leverage Molecular Dynamics (MD) simulations to forecast and scrutinize the nuanced behavior of atomic and molecular entities. Moldy, a flexible MD software, facilitated the simulation of particle trajectories and interactions across diverse scenarios, with meticulous documentation of the resulting data. For visual analytics and insight extraction, Gnuplot crafted detailed plots depicting kinetic and potential energies alongside other thermodynamic metrics over temporal scales. The integration of VMD culminated in our analysis by vividly portraying the molecular motions, enhancing comprehension of emergent patterns. This study not only endorses Moldy's precision in MD simulations but also highlights the potent alliance among simulation, analysis, and visualization in elucidating intricate particle interactions. In summary, our work underscores the efficacy of the Moldy-Gnuplot-VMD triad as a formidable resource for scientists engaged in molecular motion prediction and analysis, paving fresh paths in computational physics and chemistry research.