Biophysical Society Thematic Meeting | Hamburg 2022

Biophysics at the Dawn of Exascale Computers

Wednesday Speaker Abstracts

CONFORMATIONAL DYNAMICS AND FUNCTIONS OF PROTEINS IN CROWDED CELLULAR ENVIRONMENTS Yuji Sugita 1 ; 1 RIKEN, Cluster for Pioneering Research, Wako, Japan Recent advances of molecular dynamics (MD) simulations of biomolecules have allowed us to study protein dynamics and functions in realistic cellular environments. The cellular cytoplasm contains a large number of proteins, RNAs, metabolites, ions, and waters, suggesting that specific protein-ligand or protein-protein interactions are competing with many other off-target molecular interactions. If we include such interactions explicitly, larger number of atoms are required in the calculations, reducing the simulation time significantly. Therefore, we need to accelerate MD simulation on massively supercomputer by software optimization or parallelization. In addition, the increase of a time step to integrate the equation of motions is very effective. By introducing a theoretically accurate definition of temperature and a new hydrogen mass repartitioning scheme, we succeeded to use a 5 fs time step in the velocity Verlet integrator and a 3.5 fs fast motion time step in the multiple time step integrator without losing the stability and accuracy. These new methods were implemented into GENESIS software (https://www.r- ccs.riken.jp/labs/cbrt/) and are used now in the simulations of macromolecular crowding.

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