FPGA-Based Molecular Dynamics Simulations System Design
SU Li-li · Microelectronics & Computer · 2009
FPGA-based acceleration of Molecular Dynamics (MD) simulation,which is widely used in many fields from materials science to molecular science,has been the subject of high performance studies. The force calculations consume long time in the whole system. In this paper,we propose a system that can implement the Lennard-Jones (LJ) force computation on FPGA,and the remaining computations are computed by the host. According to the property of LJ force,we use the following methods: cell-list method,combining discrete function and interpolation for computing high power to avoid square root operation. All units organize as a pipeline to improve the performance of the system.