Paper Citing NAMD - Abstract
Guo, He; Su, Lili; Wang, Yuxin; Long, Zhu
FPGA-Accelerated Molecular Dynamics Simulations System
2009 INTERNATIONAL CONFERENCE ON SCALABLE COMPUTING AND COMMUNICATIONS & EIGHTH INTERNATIONAL CONFERENCE ON EMBEDDED COMPUTING, 360-365, 2009
Molecular Dynamics (MD) simulations, supported by parallel software and special hardware, are widely used in materials, computational chemistry and biology science. With advancing of FPGA capability and inclusion of embedded multipliers, lots of studies steer to focus on FPGA accelerated MD simulations. In this paper, we propose a system that can implement the computation on FPGA for Lennard-Jones (LJ) force which has been proved of dominating the whole execution time, and then the results are transferred to the host which takes the charge of all motion integration and other computations. To perform efficient computation on FPGA, we present two methods, one is combining discrete function and interpolation for computing high power, and the other is using Filter filtrate particles and exploiting two LJ force Calculators.
