Method generalized-ensemble

While a number of methods to enhance conformational sampling have recently been explored, the most notable of which are the class ot generalized ensemble methods (see [75] for a review), we focus on specifically on methods that take advantage of the choice of, or the coupling between, multiple alchemical intermediates. 

The first Monte Carlo study of osmotic pressure was carried out by Panagiotopoulos et al. [16], and a much more detailed study was subsequently carried out using a modified method by Murad et al. [17]. The technique is based on a generalization of the Gibbs-ensemble Monte Carlo (GEMC) method applied to membrane equihbria. The Gibbs ensemble method has been described in detail in many recent reports so we will only summarize the extension of the method to membrane equilibria here [17]. In the case of two phases separated by semi-permeable membranes... 

Hansmann, U.H.E. Okamoto, Y., Generalized-ensemble Monte Carlo method for systems with rough energy landscapes, Phys. Rev. E 1997, 56, 2228-2233... 

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 introduce the idea of the multicanonical technique into the isobaric-isothermal ensemble method and refer to this generalized-ensemble algonthnmsthemultibaric-multithermalalgorithm(MlJBAT i) [62,63,123-125]. 

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. 

An optimal choice of weights can be found by measuring the local dif-fusivity of a random walk along the reaction coordinates and applying the feedback method to shift weight towards the bottlenecks in the simulation. This generalized ensemble optimization approach has recently been illustrated for the simulation of dense Lennard-Jones fluids close to the vapor-liquid equilibrium [21]. The interaction between particles in the fluid is described by a... 

Extended ensemble methods, such as the multicanonical ensemble, Wang-Landau sampling or parallel tempering can also be generalized to quantum systems [35,36], as we will show in the next two sections. 

This review discusses a newly proposed class of tempering Monte Carlo methods and their application to the study of complex fluids. The methods are based on a combination of the expanded grand canonical ensemble formalism (or simple tempering) and the multidimensional parallel tempering technique. We first introduce the method in the framework of a general ensemble. We then discuss a few implementations for specific systems, including primitive models of electrolytes, vapor-liquid and liquid-liquid phase behavior for homopolymers, copolymers, and blends of flexible and semiflexible... 

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