Abstract:

As a novel tool to study the functions and properties of biomacromolecules, molecular dynamics has been extensively used to investigate the molecular dynamic behavior of proteins and nucleic acids. However, the time scale range of normal molecular dynamics simulation remains relatively narrow,which cannot reach the valid sampling range of biomacromolecules dynamics behavior recently. Temperature replica exchange molecular dynamics can run multiple independent simulations synchronously and effectively increase the simulating speed. Meanwhile, it requires tens of thousands of cores in aspect of the computing resources, yet the simulation systems of published literatures cannot reach such large scale hitherto. By using the 100T Flops cluster of sunway 4000A in National Supercomputing Center in Jinan, we firstly ran the molecular dynamics of single replica and then ran as many as 128 temperature replicas exchange molecular dynamics to simulate the catalytic domain of exocellulases (about 50000 atoms). We simultaneously used up to 6720 CPU cores in this task, the total computing speed accumulated to 2274ns／d, which offers a new approach to run the molecular dynamics over ten thousand CPU cores.

Key words: molecular dynamics simulation; replica exchange; hundred trillion times; Sunway 4000A; deployment and optimization