Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations
Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations
复制标题
分子动力学机：分子动力学模拟专用计算机
DOI：
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发表时间：
1999
期刊：
影响因子：
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通讯作者：
B. Elmegreen
中科院分区：
文献类型：
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作者：
T. Narumi;R. Susukita;T. Ebisuzaki;G. D. McNiven;B. Elmegreen
摘要我们正在开发分子动力学机器(MDM)，这是一台用于经典分子动力学模拟的专用计算机。当我们在不截断库仑力的情况下处理一个大的带电粒子系统时，由于库仑力的计算代价控制了总的计算时间，因此加速了非键力、库仑力和范德华力的计算。当我们使用Ewald方法时，库仑力可以通过将其分为实空间部分和波数空间部分来计算。MDM由MDGRAPE-2、WINE-2和主机组成。MDGRAPE-2计算范德华力和库仑力的实空间部分。WINE-2计算库仑力的波数空间部分。主机计算键合力，并更新原子的位置和速度。MDM的目标性能为100TFLOPS，在实际应用中将维持约30TFLOPS。它可以在一周内计算一百万个原子的MD模拟的3.2×106个时间步长。整个系统将是完整的..。
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 complete...