Replica-permutation method to enhance sampling efficiency

Abstract

In order to predict the native structures of proteins and peptides and to investigate the functions of these biomolecules, it is essential to realise efficient sampling in the conformational space. We had recently proposed a new generalised-ensemble algorithm, which is referred to as the replica-permutation method (RPM), to sample the conformational space efficiently. We introduce this RPM and demonstrate its usefulness by applying to three systems: particles in a double-well potential energy, Met-enkephalin in a vacuum, and a C-peptide analogue of ribonuclease A in explicit water. Replica-exchange simulations were performed to compare their results with the results of the replica-permutation simulations. It is shown that the RPM sampled not only the temperature space but also the conformational space more efficiently than the replica-exchange method. The folding pathway of C-peptide is also presented.

Keywords::

• molecular dynamics
• Monte Carlo
• replica-permutation method
• generalised ensemble

Acknowledgements

The computations were performed on the computers at the Research Center for Computational Science, Okazaki Research Facilities, National Institutes of Natural Sciences. This work was supported by the JSPS KAKENHI Grant Number 24740296.