Prof. Satoru G. Itoh (IMS), Prof. Hisashi Okumura (IMS) and Prof. Y. Okamoto (Nagoya U.) recently proposed a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter is exchanged.
Effective samplings in the conformational space are necessary to predict the native structures of proteins. The replica-exchange method is one of the most well-known methods among the generalized-ensemble algorithms which realize effective samplings in the conformational space for biomolecular systems. However, the replica-exchange method has a difficulty for large systems that many replicas are needed to realize such effective samplings. In other words, huge amount of computation time is required in the replica-exchange method for the large systems.
In order to overcome this difficulty, we recently proposed a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter is exchanged although the temperature is exchanged in conventional replica-exchange method. By decreasing the van der Waals radii, which control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers for biomolecule systems. Furthermore, the simulation based on this method escapes from the free-energy local-minimum states and realizes effective samplings in the conformational space of the biomolecule systems. We applied this method to an alanine dipeptide in aqueous solution and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical and replica-exchange methods.
We will apply such an effective sampling method to the protein folding problem in the future. Aims of our research group are to predict the native structure of a protein with more than 50 amino acid residues and understand how the protein forms the tertiary structure.
Paper Information
Journal: J. Chem. Phys. 132 134105 (2010)
Title: Replica-exchange method in parameter space: overcoming steric restrictions for biomolecules
Author: Satoru G. Itoh, Hisashi Okumura, Yuko Okamoto
