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Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency
Author(s) -
Fukuhara Daiki,
Yamauchi Masataka,
Itoh Satoru G.,
Okumura Hisashi
Publication year - 2023
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.27020
Subject(s) - replica , permutation (music) , sampling (signal processing) , computer science , statistical physics , mathematics , algorithm , physics , art , filter (signal processing) , acoustics , visual arts , computer vision
In the replica‐permutation method, an advanced version of the replica‐exchange method, all combinations of replicas and parameters are considered for parameter permutation, and a list of all the combinations is prepared. Here, we report that the temperature transition probability depends on how the list is created, especially in replica permutation with solute tempering (RPST). We found that the transition probabilities decrease at large replica indices when the combinations are sequentially assigned to the state labels as in the originally proposed list. To solve this problem, we propose to modify the list by randomly assigning the combinations to the state labels. We performed molecular dynamics simulations of amyloid‐β(16–22) peptides using RPST with the “randomly assigned” list (RPST‐RA) and RPST with the “sequentially assigned” list (RPST‐SA). The results show the decreases in the transition probabilities in RPST‐SA are eliminated, and the sampling efficiency is improved in RPST‐RA.