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The 193rd R-CCS Cafe - part 2

Title

GENESIS 2.0 for Biomolecular Simulations

Details
Date Mon, Jul 6, 2020
Time 4:20 pm - 4:40 pm (5:05 pm - 5:20 pm　Free discussion with speakers, 5:20 pm -　Free discussion)
City Kobe, Japan
Place

Online seminar on BlueJeans

  • If you are not affiliated with R-CCS and would like to attend R-CCS Cafe, please email us at r-ccs-cafe[at]ml.riken.jp.
Language Presentation Language: English
Presentation Material: English
Speakers

Yuji SUGITA

Team Leader, Computational Biophysics　Research Team

photo:Yuji SUGITA

Abstract

We have developed GENESIS software for biomolecular dynamics simulations for the last ten years. Originally, it was designed to utilize K computer, while it is also available on Intel CPU cluster, Intel KNL, and NVIDIA GPU clusters. Since Fugaku, the world fastest supercomputer in 2020, is composed of ARM CPU, we had to optimize GENESIS to Fugaku ARM architecture for the last few years. Co-design between system and application developers has worked well for this purpose. We could achieve significant acceleration of MD simulations using GENESIS on Fugaku compared to the same calculation on K computer. The accuracy in MD simulations has also been improved by introducing more accurate definitions of system temperature and pressure in MD simulations. This allows us to use a longer time step to integrate the equations of motion, suggesting a better performance than the standard simulation conditions. Using GENESIS 2.0 on Fugaku, protein dynamics in longer time scales and in realistic cellular environments is possible for better understanding of structure-dynamics-function relationships in biomacromolecules.

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（Jun 30, 2020）