Adenosine triphosphate (ATP) is the fuel of life; every living cell must use ATP to carry out its functions, and the human body synthesizes its own weight in ATP every day. The ubiquitous molecular motor ATP synthase catalyzes the creation of ATP by precisely directing electrochemically generated torque. A detailed understanding of how this system functions can impact areas ranging from neurodegenerative disease research to nanotechnology development. Running at the Pittsburgh Supercomputing Center on LeM ieux, the most powerful computer system in the world for open research, the freely available simulation code NAMD can simulate a solvated all-atom model of ATP synthase with full electrostatics at 65% efficiency on 1000 processors. This achievement in scalability places NAMD an order of magnitude ahead of comparable packages for molecular dynamics simulation.