Construction and Optimization of GPU-Based Computing Platform for Biological Macromolecules

Abstract:

Biological macromolecules by molecular dynamics computing platform for analog operation，calculated value can describe the trajectory of molecules，which reveals the intrinsic relationship between atoms，but the process is more complicated and expensive. In this paper，the construction and optimization to achieve lower investment macromolecules computing platforms，using a software package AMBER molecular dynamics simulation runs in parallel GPU and CUDA system conditions. Through the operation of two large molecules，experimental results show that the computing platform reached 60 times the computing speed up to achieve a high acceleration performance，completed the construction of cost-effective，high-performance computing platform.