Abstract
The native structure of protein corresponds to the global minimum of free energy. Replica-exchange method (REM) has been recently used to search the energy minimum in a huge conformation space of a protein. For large systems, however, applying REM can be costly since the number of replicas required for the conformation sampling increases. We have developed a variant REM called fragment REM (FREM), which is based on the existence of correlation between the local amino acid sequence and the local structure. Equilibrium distributions for poly-alanine were computed by the conventional MD, REM and the proposed FREM simulations. We have found that FREM successfully reduces the number of replicas needed for the simulation.
