Performance Analysis for Molecular Dynamics Simulation on an SGI Altix Supercomputer

Fast Fourier Transforms (FFTs) are often used in Molecular Dynamics (MD) simulations to calculate force fields of interacting atoms and molecules. A performance analysis shows that the computation time and the communication time of the FFT in MD is not insignificant. Exponential speedup of FFTs, with a quantum computation platform, has been described. Until recently the ability to send classical data into, and retrieve classical data from a quantum computing device capable of performing an FFT has been problematic. Recent achievements suggest that this problem is close to solution. In this encouraging context, this paper explores the performance improvement that might be expected by use of a quantum implementation of FFT in Molecular Dynamics algorithms.