Monte Carlo methods protocols

The multiple-round, Monte Carlo protocols appear to be especially effective on the more difficult systems with larger numbers of composition and noncomposition variables. That is, the Monte Carlo methods have a tremendous advantage over one-pass methods, especially as the number of variables increases, with parallel tempering the best method. The Monte Carlo... 

Fig. 5. The maximum figure of merit found with different protocols on systems with different number of composition (x) and noncomposition (z) variables (from Falcioni and Deem, 2000). The results are scaled to the maximum found by the grid searching method. Each value is averaged over scaled results on 10 instances of the random phase volume model with different random phases. The Monte Carlo methods are especially effective on systems with a larger number of variables, where the maximal figures of merit are more difficult to locate.

Several remedies have been suggested for improving the PB based pKa prediction methods. Most of them are based on strategies that combine conformational flexibility with the PB calculation. You and Bashford included multiple conformers by systematically scanning the side chain torsion angles [107], Alexov and Gunner used Monte-Carlo protocol to sample positions of hydroxyl and other polar protons [1], This method, referred to as the multi-conformation continuum electrostatic (MCCE), was later extended to include rotamers for residues that have strong electrostatic... 

This text focuses on applications, with only passing mention of the mechanics of modeling the descriptions of the intermolecular or interatomic interactions, the methods of quantum and classical mechanics and the protocols such as energy minimization, Monte Carlo or molecular dynamics that are the basis for computing structures and properties. These are discussed in var3dng degrees of detail in other instructional texts, to which the reader is referred for further background [7-10]. 

The effective use of temperature as a control factor in the Metropolis Monte Carlo process is the most important factor for the success of simulated annealing method. This has inspired an attempt to exploit temperature in a new way. Von Freyberg [21] has proposed a Simulated Shocking protocol for the efficient search for conformations of polypeptides. In this protocol, the temperature jumps between a very low (T = 5 K) and very high temperature... 

The recommended error estimation methods for high volatility compounds from the reference are reviewed in this section of the report after describing the test protocol procedures. A Monte Carlo simulation of experimental results was then performed followed by statistical analyses to determine the distribution and amount of error associated with estimation of volatilization from water for a high volatility compound. 

An obvious way to combine Monte Carlo with molecular d)mamics is to use each technique for the most appropriate part of a simulation. For example, when simulating a solvated macromolecule, the equilibration phase is usually performed in a series of stages. In the first stage, the solute is kept fixed while the solvent molecules (and any ions, if present) are allowed to move under the influence of the solute s electrostatic field. This solvent equilibration may often be performed more effectively using a Monte Carlo simulation as the solvent and ions do not have any appreciable conformational flexibility. To simulate the whole system, molecular d)maimcs is then the most appropriate method. Such a protocol has been used to perform long simulations of DNA molecules [Swaminathan et al. 1991]. 

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