The 209th R-CCS Cafe - part 1

In the computational biophysics research team, we have developed GENESIS molecular dynamics software for biological systems. Using GENESIS, multi-scale simulations using atomistic, coarse-grained, and QM/MM models are available and its performance on Fugaku has been optimized via co-design strategy in Flagship 2020 project. Last year, we performed extensive molecular dynamics simulations of SARS-CoV-2 spike protein using GENESIS on Fugaku. In MD simulations from the down or up structures, we elucidated the functional roles of glycans on the surface of the spike protein. We also applied the gREST method, which is one of the enhanced sampling methods developed in our group, to the spike-protein dynamics, aiming to simulate large-scale conformational changes between the down and up structures. The intermediate structures and transition pathways were obtained in the simulations.