Generalized-Ensemble Algorithms

Mitsutake, A. Sugita, Y. Okamoto, Y., Generalized-ensemble algorithms for molecular simulations of biopolymers, Biopolymers 2001, 60, 96-123... 

Generalized-Ensemble Algorithms for Studying Protein Folding... 

In this article, we describe the generalized-ensemble algorithms mentioned earlier. Namely, we first review the two familiar methods MUCA and REM. We then describe multidimensional extensions of these methods. Examples of the results by some of these algorithms are then presented. 

We now present some of the simulation results by the generalized-ensemble algorithms that were described in the previous section. 

In this article, we have reviewed some of powerful generalized-ensemble algorithms for both Monte Carlo simulations and molecular dynamics simulations. A simulation in generalized ensemble realizes a random walk in potential energy space, alleviating the multiple-minima problem that is a common difficulty in simulations of complex systems with many degrees of freedom. 

Detailed formulations of the two well-known generalized-ensemble algorithms, namely, multicanonical algorithm (MUCA) and replica-exchange method (REM), were given. We then introduced further extensions of the above two methods. We have shown the effectiveness of these algorithms by applying them to various biomolecular systems. 

Okamoto, Y. Generalized-ensemble algorithms Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graph. Model. 2004, 22, 425-39. 

In this section, we briefly describe our hybrid approach for predicting conformations of biomolecules stabilized in solvent [15, 16, 17]. In this approach, the RISM theory is combined with the MC simulated annealing or one of the generalized-ensemble algorithms. Our approach falls into the third category, and both the biomolecule and the solvent are treated on the atomic level. The hybrid approach is implemented for two small peptides as the first step of the research. The solvent effects on the conformational stability of the peptides are discussed and the... 

In a preliminary prediction of a peptide conformation, the conformational entropy of the peptide is often neglected, and we follow this custom. Our aim is to determine the most stable conformation of a peptide molecule in solvent, and in this case the MC simulated annealing is a powerful tool. To obtain information on the average conformation by accounting for the conformational entropy, one needs to employ a generalized-ensemble algorithm. The combination of the RISM theory and the multi-canonical algorithm is considered in 1.8. 

Okamoto, Y. Tackling the multiple-minima problem in protein folding by Monte Carlo simulated annealing and generalized-ensemble algorithms. Int. J. Mod. Phys. C 1999, 10 (8), 1571-1582. 

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