TY - JOUR
T1 - Simulated-tempering replica-exchange method for the multidimensional version
AU - Mitsutake, Ayori
N1 - Funding Information:
The author would like to thank Professor Yuko Okamoto in Nagoya University, Japan and Professor Hiroshi Takano in Keio University, Japan for discussions with this work. Some of the results were obtained by the computations on the supercomputers at the Institute for Molecular Science, Okazaki, Japan. This work was supported, in part, by Grants-in-Aid for Scientific Research in Priority Areas (“Water and Biomolecules”) and for the Next Generation Super Computing Project, Nanoscience Program from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan.
PY - 2009
Y1 - 2009
N2 - In this article, the general formulation of the multidimensional simulated-tempering replica-exchange method is described. In previous works, the one-dimensional replica-exchange simulated-tempering and simulated-tempering replica-exchange methods were developed. For the former method, the weight factor of the one-dimensional simulated tempering is determined by a short replica-exchange simulation and multiple-histogram reweighing techniques. For the latter method, the production run is a replica-exchange simulation with a few replicas not in the canonical ensembles but in the simulated-tempering ensembles which cover wide ranges of temperature. Recently, the general formulation of the multidimensional replica-exchange simulated tempering was presented. In this article, the extension of the simulated-tempering replica-exchange method for the multidimensional version is given. As an example of applications of the algorithm, a two-dimensional replica-exchange simulation and two simulated-tempering replica-exchange simulations have been performed. Here, an α -helical peptide system with a model solvent has been used for the applications.
AB - In this article, the general formulation of the multidimensional simulated-tempering replica-exchange method is described. In previous works, the one-dimensional replica-exchange simulated-tempering and simulated-tempering replica-exchange methods were developed. For the former method, the weight factor of the one-dimensional simulated tempering is determined by a short replica-exchange simulation and multiple-histogram reweighing techniques. For the latter method, the production run is a replica-exchange simulation with a few replicas not in the canonical ensembles but in the simulated-tempering ensembles which cover wide ranges of temperature. Recently, the general formulation of the multidimensional replica-exchange simulated tempering was presented. In this article, the extension of the simulated-tempering replica-exchange method for the multidimensional version is given. As an example of applications of the algorithm, a two-dimensional replica-exchange simulation and two simulated-tempering replica-exchange simulations have been performed. Here, an α -helical peptide system with a model solvent has been used for the applications.
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U2 - 10.1063/1.3204443
DO - 10.1063/1.3204443
M3 - Article
C2 - 19739847
AN - SCOPUS:69949183901
VL - 131
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 9
M1 - 094105
ER -