Biomolecules (esp., proteins) have various functions (transportation/recognition/skeleton) in the cell. We have studied these, including the proton transport function of cytochrome c oxidase (J. Am. Chem. Soc. 2012) and antigen-recognition function of antibody (Protein Sci. 2015) by using the molecular dynamics simulation. We aim to analyze and understand how atom-level dynamics lead to the supermolecular function with supercomputers.