Journal Club: Sampling the stable structures based on replica-permutation method

When we want to search the (meta)stable structures of the macromolecules such as protein, the combination of molecular dynamics simulation and replica exchange method (REM) is useful. In REM, sampling is performed by exchanging replicas (copies) of the system having different temperatures when this process is accepted based on Metropolis algorithm. In this method, the exchange can be rejected, which leads to the decrease in the sampling efficiency. To obtain more efficient sampling than that of REM, Itoh and Okumura proposed replica-permutation method (RPM) in which the replicas are permutated to perform sampling based on Suwa-Toudou algorithm. In this Journal club, I will introduce RPM and some examples of its application.