In Computational Biophysics Research Team, RIKEN R-CCS, we have developed GENESIS (GENeralized-Ensemble SImulation System) for understanding and predicting dynamic processes in chemical and biological systems. GENESIS is software for molecular dynamics (MD) simulations based on QM/MM, atomistic, and coarse-grained molecular models. GENESIS shows one of the best performances for large-scale MD simulations of biological systems using many CPU cores and GPUs in recent computers. For this, we have developed a number of computational algorithms in MD simulation and optimized the codes to K, FUGAKU, or other massively parallel supercomputers with/without GPUs. The development of GENESIS has been done in collaboration with Theoretical Molecular Science Laboratory, RIKEN CPR and Laboratory for Biomolecular Function Simulation, RIKEN BDR.
We have also developed a machine learning approach to connect MD simulation with single-molecule experiments for examining biomolecular folding and dynamics without suffering from molecular force field biases.
We have also developed a machine learning approach to connect MD simulation with single-molecule experiments for examining biomolecular folding and dynamics without suffering from molecular force field biases.
Lead Researcher: Yuji Sugita
(Computational Biophysics Research Team)
(Computational Biophysics Research Team)
