Fast algorithm/ hardware joint acceleration for molecular dynamics simulations and its efficacy confirmation

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Molecular dynamics simulation provides valuable means to study the structure and dynamics of molecular systems. Since it demands vast computational resources, particularly when it is applied to large biological systems, it presents challenging problems to computational technology. Although several fast algorithms were developed for reducing the computation time, these algorithms encounter certain difficulties.To overcome this problem, in this work, I developed algorithms that realized efficient cooperation of dedicated computational board (MD-Engine II) with fast algorithms, such as fast multipole method (FMM). The algorithms were implemented on a PC, into which the computation boards were plugged, to acutally build up a specialized computation unit for MD simulations. I then developed a cluster of the four computation units to realize a high performace system for accurate MD calculation at low cost. Using the computation system, 1MD step of a protein-water system (fifty thousand atoms) can be completed in 1.6s. In addition, the results of a series of 50 ps MD simulations of a protein-water system (fifty thousand atoms) revealed that a more stringent setting of accuracy in FMM computation, as compared with those previously reported, was required for accurate simulations over long time periods.