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Replica sub‐permutation method for molecular dynamics and monte carlo simulations
Author(s) -
Yamauchi Masataka,
Okumura Hisashi
Publication year - 2019
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.26030
Subject(s) - monte carlo method , statistical physics , replica , molecular dynamics , permutation (music) , monte carlo molecular modeling , dynamic monte carlo method , kinetic monte carlo , computer science , hybrid monte carlo , monte carlo method in statistical physics , markov chain monte carlo , physics , computational chemistry , mathematics , chemistry , statistics , art , acoustics , visual arts
We propose an improvement of the replica‐exchange and replica‐permutation methods, which we call the replica sub‐permutation method (RSPM). Instead of considering all permutations, this method uses a new algorithm referred to as sub‐permutation to perform parameter transition. The RSPM succeeds in reducing the number of combinations between replicas and parameters without the loss of sampling efficiency. For comparison, we applied the replica sub‐permutation, replica‐permutation, and replica‐exchange methods to a β ‐hairpin mini protein, chignolin, in explicit water. We calculated the transition ratio and number of tunneling events in the parameter space, the number of folding–unfolding events, the autocorrelation function, and the autocorrelation time as measures of sampling efficiency. The results indicate that among the three methods, the proposed RSPM is the most efficient in both parameter and conformational spaces. © 2019 Wiley Periodicals, Inc.