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The 221st R-CCS Cafe - part 3

Japanese

Title

Optimization of GENESIS MD software on Fugaku

Details
Date Fri, Nov 12, 2021
Time 4:40 pm - 5:00 pm (5 pm - 5:20 pm　Discussion, 5:20 pm - Free discussion (optional))
City Online
Place

Online seminar on BlueJeans

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Language Presentation Language: English
Presentation Material: English
Speakers

Jaewoon Jung

Research Scientist, Computational Biophysics Research Team

Abstract

We introduce new parallel computing algorithms in the GENESIS software to perform cellular-scale molecular dynamics (MD) simulations on Fugaku. It includes (1) the new algorithm of real-space non-bonded interactions, (2) reciprocal-space non-bonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems.Based on these developments, GENESIS can perform MD simulations of the system containing 1.6 billion atoms with the performance of 8.30 ns/day. It will extend the available size and time of MD simulations to answer unresolved questions of biomolecules in a living cell.

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（Nov 11, 2021）