We develop software to perform molecular dynamics (MD) simulations and QM/MM calculations using massively parallel supercomputers like K supercomputer. The software is now optimized to K computer and shows high parallel efficiency in MD simulations. We also introduce the generalized-ensemble simulation methods or other enhanced techniques into the software for improving the performance of simulations.
GENESIS (GENeralized Ensemble SImulation Systems) is the name of software, which we are developing for simulations using K computer. In GENESIS, generalized-ensemble simulations like replica-exchange molecular dynamics are available for coarse-grained, atomistic, and QM/MM models. We improve the efficiency of parallelization in GENESIS for K computer and plan to open the first version of GENESIS in few years.
X-ray free electron laser (XFEL) is an X-ray combining the feature of laser at free electron state, and is built in RIKEN Harima Institute. We collaborate with Computational structural biology unit at RIKEN AICS for developing refinement software for XFEL data using K computer. We simulate large-scale biological systems (from 10 nm to µm in size) using structural data observed with XFEL experiments.
Single-molecule experiments on biological molecules are now widely used to observe molecular and cellular dynamics. We combine low-dimensional trajectories of single-molecule experiments with molecular simulations for getting much detailed information of the target molecular motions. As a theoretical basis, we can use the theory of data assimilation that is widely used in weather forecast or other research areas.
