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Molecular dynamics (MD) models require comprehensive computational power to simulate nanoscale phenomena. Traditionally, central processing unit (CPU) clusters have been the standard method of performing these numerically intensive computations. This article investigates the use of graphical processing units (GPUs) to implement large-scale MD models for exploring nanofluidic-substrate interactions. MD models of water nanodroplets over flat silicon substrate are tracked wherein the simulation attains a steady state computational performance. Different classes of GPU units from NVIDIA (C2050, K20, and K40) are evaluated for energy efficiency performance with respect to three green computing measures: simulation completion time, power consumption, and CO2 emissions. The CPU+K40 configuration displayed the lowest energy consumption profile for all the measures. This research demonstrates the use of energy efficient graphical computing versus traditional CPU computing for high-performance molecular dynamics simulations.