Comparison of Replica-Permutation Molecular Dynamics Simulations with and without Detailed Balance Condition

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Hiroaki Nishizawa¹, and Hisashi Okumura¹^,²^,

+ Affiliations

¹Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan²Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan

Received March 24, 2015; Accepted May 19, 2015; Published June 25, 2015

In the replica-permutation method (RPM), temperatures are not only exchanged between two replicas but also permutated among more than two replicas using the Suwa–Todo algorithm, which minimizes the rejection ratio in Monte Carlo trials. We verify the sampling efficiency of RPM that adopts Suwa–Todo algorithms with and without a detailed balance condition (DBC). To compare these techniques, molecular dynamics simulations of RPM with and without the DBC and the replica-exchange method (REM) were carried out for a chignolin molecule in explicit water. Although no difference in the numbers of folding and unfolding events was observed, the numbers of tunneling events of the two RPM simulations were larger than that of REM. This indicates that the minimization of the rejection ratio by the Suwa–Todo algorithm in RPM realizes efficient sampling. Furthermore, the sampling efficiency was slightly higher in the RPM without the DBC than in that with the DBC. The reason for this difference is also discussed.

https://doi.org/10.7566/JPSJ.84.074801

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Comparison of Replica-Permutation Molecular Dynamics Simulations with and without Detailed Balance Condition

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