R-CCS Cafe 第221回 第3部

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.