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Hamiltonian replica‐permutation method and its applications to an alanine dipeptide and amyloid‐β(29–42) peptides
Author(s) -
Itoh Satoru G.,
Okumura Hisashi
Publication year - 2013
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.23402
Subject(s) - replica , dipeptide , hamiltonian (control theory) , coulomb , monte carlo method , hybrid monte carlo , statistical physics , chemistry , physics , markov chain monte carlo , mathematics , quantum mechanics , peptide , biochemistry , art , mathematical optimization , statistics , visual arts , electron
We propose the Hamiltonian replica‐permutation method (RPM) (or multidimensional RPM) for molecular dynamics and Monte Carlo simulations, in which parameters in the Hamiltonian are permuted among more than two replicas with the Suwa‐Todo algorithm. We apply the Coulomb RPM, which is one of realization of the Hamiltonian RPM, to an alanine dipeptide and to two amyloid‐β(29–42) molecules. The Hamiltonian RPM realizes more efficient sampling than the Hamiltonian replica‐exchange method. We illustrate the protein misfolding funnel of amyloid‐β(29–42) and reveal its dimerization pathways. © 2013 Wiley Periodicals, Inc.