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The interface between two of the NQR subunits, NqrB and NqrD, has been proposed to harbor a binding site for inhibitors of Na<jats:sup>+<\/jats:sup>-NQR. While the mechanisms underlying Na<jats:sup>+<\/jats:sup>-NQR function and inhibition remain underinvestigated, their clarification would facilitate the design of compounds suitable for clinical use against pathogens containing Na<jats:sup>+<\/jats:sup>-NQR. An in silico model of the NqrB\u2013D interface suitable for use in molecular dynamics simulations was successfully constructed. A combination of algorithmic and manual methods was used to reconstruct portions of the two subunits unresolved in the published crystal structure and validate the resulting structure. Hardware and software optimizations that improved the efficiency of the simulation were considered and tested. The geometry of the reconstructed complex compared favorably to the published <jats:italic>V. cholerae<\/jats:italic> Na<jats:sup>+<\/jats:sup>-NQR crystal structure. Results from one 1\u00a0\u00b5s, three 150\u00a0ns and two 50\u00a0ns molecular dynamics simulations illustrated the stability of the system and defined the limitations of this model. When placed in a lipid bilayer under periodic boundary conditions, the reconstructed complex was completely stable for at least 1\u00a0\u00b5s. 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