Student Posters Repository

 Molecular dynamics simulation is a powerful tool to study biomolecules. However, sometimes their configurations get trapped in local minimum of free energy landscape and it prevents us from efficient simulations. To overcome this problem, replica-exchange method and replica-permutation method have been proposed. Replica-permutation method is an improved alternative of the replica-exchange method. However, volume cannot be changed in previous replica-permutation method. In this study, I developed the replica-permutation method in the isothermal-isobaric ensemble. The isothermal-isobaric replica-permutation method carries out many molecular dynamics simulations (replicas) at the same time, and sometimes the parameters such as temperatures and pressures are permuted among the replicas through MPI communication. The replica-permutation methods use the Suwa-Todo algorithm to permute parameter labels instead of the Metropolis algorithm so that the rejection rate can be minimized. I showed that the method enhances the sampling efficiency.