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2023-01-16T04:17:34Z
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Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test
Mitsutake, Ayori
Sugita, Yuji
Okamoto, Yuko
open access
Copyright 2003 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing.The following article appeared in (The Journal of Chemical Physics. v.118, n.14, 2003, p.6664-6675) and may be found at (http://dx.doi.org/10.1063/1.1555847).
The replica-exchange multicanonical algorithm and the multicanonical replica-exchange method for molecular dynamics simulations have recently been developed. In the former method the multicanonical weight factor is determined from a short replica-exchange simulation with the multiple-histogram reweighting techniques. A long multicanonical production run with high statistics is then performed with this weight factor. In this method, the process of determining the multicanonical weight factor is faster and simpler than that in the usual iterative determination. The multicanonical replica-exchange method is a further extension of the first in which a replica-exchange multicanonical simulation is performed with a small number of replicas. In this paper, we give the formulations of these two methods for Monte Carlo simulations and demonstrate the effectiveness of these algorithms for a penta peptide in the gas phase.
AIP Publishing
2003-04-08
eng
journal article
VoR
http://hdl.handle.net/2237/00029121
https://nagoya.repo.nii.ac.jp/records/26918
https://doi.org/10.1063/1.1555847
0021-9606
The Journal of Chemical Physics
118
14
6664
6675
https://nagoya.repo.nii.ac.jp/record/26918/files/1_1555847.pdf
application/pdf
351.3 kB
2018-12-17