Generalized-ensemble simulations of spin systems and protein systems

DOI10.1016/S0010-4655(02)00436-8MaRDI QIDQ1613745zbMATHWikidataFDO

Authors Takehiro Nagasima, Yuji Sugita, Ayori Mitsutake, Yuko Okamoto

Publication date 2 September 2002

Published in Computer Physics Communications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/cond-mat/0111588

zbMATH Keywords

Potts modelsimulated temperingprotein foldingmulticanonical algorithmgeneralized-ensemble algorithmreplica-exchange method

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Lattice systems (Ising, dimer, Potts, etc.) and systems on graphs arising in equilibrium statistical mechanics (82B20)

Abstract: In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the generalized-ensemble algorithms in order to overcome this multiple-minima problem. Three well-known generalized-ensemble algorithms, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described. We then present three new generalized-ensemble algorithms based on the combinations of the three methods. Effectiveness of the new methods are tested with a Potts model and protein systems.

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Cites work

• Monte Carlo study of the interacting self-avoiding walk model in three dimensions.

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