Accelerator board for great speed up molecular dynamics (MD) simulations -(2002) Fuji Xerox developed a high-speed, precision accelerator board, MD Engine II, to carry out computer simulations based on molecular dynamics. MD Engine II includes a maximum of 19 boards that are connected to achieve 76 gigaflops, the same processing power of a supercomputer. In order to do an MD simulation, it is necessary to calculate non-bonded interactions, such as Coulombic force or van der Waals (v.d.W) force.In most MD simulation cases, over 90% of simulation time is spent to calculate these interactions. Especially, when coulombic interaction works, over 99% of calculation time is spent for it. This is the main cause to which it takes a long time for the MD simulations. A cheap method cut-off of the long-range interaction is often adopted. However, another problem with low reliability of the simulation result is often caused in this method. MD Engine II enables high-speed computations of non-bonded interactions, thus significantly reduces the computing time for many MD simulation applications. (MD, MD Engine, accelerator, parallel calculation, molecular dynamics, simulation, protein, pc cluster)
