Alignment methods for biased multicanonical sampling.
نویسندگان
چکیده
The efficiency of the multicanonical procedure can be significantly improved by applying an additional bias to the numerically generated sample space. However, results obtained by biasing in different sampling regions cannot in general be accurately combined, since their relative normalization coefficient is not known precisely. We demonstrate that for overlapping biasing regions a simple iterative procedure can be employed to determine the required coefficients.
منابع مشابه
Multicanonical methods, molecular dynamics, and Monte Carlo methods: Comparison for Lennard-Jones glasses
We applied a multicanonical algorithm to a two-dimensional and a three-dimensional Lennard-Jones system with quasicrystalline and glassy ground states. Focusing on the ability of the algorithm to locate low-lying energy states, we compared the results of the multicanonical simulations with standard Monte Carlo simulated annealing and molecular-dynamics methods. We find slight benefits to using ...
متن کاملMulticanonical MCMC for sampling rare events: an illustrative review
Multicanonical MCMC (Multicanonical Markov Chain Monte Carlo; Multicanonical Monte Carlo) is discussed as a method of rare event sampling. Starting from a review of the generic framework of importance sampling, multicanonical MCMC is introduced, followed by applications in random matrices, random graphs, and chaotic dynamical systems. Replica exchange MCMC (also known as parallel tempering or M...
متن کاملReplica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical weight factor. In this method a short replica-exchange simulation is performed and the multicanonical weight factor is obtained by the multiple-histogram reweighting techniques. The second one is a further extension of...
متن کاملMulticanonical Monte Carlo calculation of the free-energy map of the base-amino acid interaction
The specific interactions between base pairs and amino acids were studied by the multicanonical Monte Carlo method. We sampled numerous interaction configurations and side-chain conformations of the amino acid by the multicanonical algorithm, and calculated the free energies of the interactions between an amino acid at given Cα positions and a fixed base pair. The contour maps of free energy de...
متن کاملFree-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replicaexchange method; the latter is also referred to as parallel tempering. We present a new generalized-ensemble algorithm that combines the merits of the two methods; it is referred to as the replica-exchange multicanonical alg...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Journal of the Optical Society of America. A, Optics, image science, and vision
دوره 24 8 شماره
صفحات -
تاریخ انتشار 2007