Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations

Publisher Website
Google Scholar
Abstract
We are now developing Molecular Dynamics Machine (MDM), a special-purpose computer for classical molecular dynamics simulations. It accelerates the calculation of non-bonding force, Coulomb and van der Waals forces, because the calculation cost for Coulomb force dominates the total calculation time when we treat a large system of charged particles without truncating Coulomb force. When we use Ewald method, the Coulomb force can be calculated by dividing it into real-space and wavenumber-space parts. MDM is composed of MDGRAPE-2, WINE-2, and a host computer. MDGRAPE-2 calculates van der Waals force and real-space part of Coulomb force. WINE-2 calculates wavenumber-space part of Coulomb force. The host computer calculates bonding-force and updates positions and velocities of atoms. The target performance of MDM is 100 Tflops and will sustain about 30 Tflops in realistic applications. It can calculate 3.2 × 106 time-steps of MD simulation with a million atoms in a week. Total system will be completed in 1999.