TY - JOUR

T1 - Multidimensional generalized-ensemble algorithms for complex systems

AU - Mitsutake, Ayori

AU - Okamoto, Yuko

N1 - Funding Information:
Some of the results were obtained by the computations on the super computers 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 “Molecular Theory for Real Systems”), for Scientific Research on Innovative Areas (“Fluctuations and Biological Functions”), 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 - We give general formulations of the multidimensional multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function E0 by adding any physical quantity V of interest as a new energy term. These multidimensional generalized-ensemble algorithms then perform a random walk not only in E0 space but also in V space. Among the three algorithms, the replica-exchange method is the easiest to perform because the weight factor is just a product of regular Boltzmann-like factors, while the weight factors for the multicanonical algorithm and simulated tempering are not a priori known. We give a simple procedure for obtaining the weight factors for these two latter algorithms, which uses a short replica-exchange simulation and the multiple-histogram reweighting techniques. As an example of applications of these algorithms, we have performed a two-dimensional replica-exchange simulation and a two-dimensional simulated-tempering simulation using an α -helical peptide system. From these simulations, we study the helix-coil transitions of the peptide in gas phase and in aqueous solution.

AB - We give general formulations of the multidimensional multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function E0 by adding any physical quantity V of interest as a new energy term. These multidimensional generalized-ensemble algorithms then perform a random walk not only in E0 space but also in V space. Among the three algorithms, the replica-exchange method is the easiest to perform because the weight factor is just a product of regular Boltzmann-like factors, while the weight factors for the multicanonical algorithm and simulated tempering are not a priori known. We give a simple procedure for obtaining the weight factors for these two latter algorithms, which uses a short replica-exchange simulation and the multiple-histogram reweighting techniques. As an example of applications of these algorithms, we have performed a two-dimensional replica-exchange simulation and a two-dimensional simulated-tempering simulation using an α -helical peptide system. From these simulations, we study the helix-coil transitions of the peptide in gas phase and in aqueous solution.

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U2 - 10.1063/1.3127783

DO - 10.1063/1.3127783

M3 - Article

C2 - 19508054

AN - SCOPUS:67249165701

SN - 0021-9606

VL - 130

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

IS - 21

M1 - 214105

ER -