منابع مشابه
Umbrella sampling
The calculation of free-energy differences is one of the main challenges in computational biology and biochemistry. Umbrella sampling, biased molecular dynamics (MD), is one of the methods that provide free energy along a reaction coordinate. Here, the method is derived in a historic overview and is compared with related methods like thermodynamic integration, slow growth, steered MD, or the Ja...
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A new method has been developed to approximate one Gaussian mixture by another in a process that generalizes the idea of importance re-sampling in a particle filter. This algorithm is being developed as part of an effort to generalize the concept of a particle filter. In a traditional particle filter, the underlying probability density function is described by particles: Dirac delta functions w...
متن کاملUmbrella sampling for nonequilibrium processes.
The authors introduce an algorithm for determining the steady-state probability distribution of an ergodic system arbitrarily far from equilibrium. By enforcing equal sampling of different regions of phase space, as in umbrella sampling simulations of systems at equilibrium, low probability regions are explored to a much greater extent than in physically weighted simulations. The algorithm can ...
متن کاملMarginal likelihoods for non-Gaussian models using auxiliary mixture sampling
Several new estimators of the marginal likelihood for complex non-Gaussian models are developed. These estimators make use of the output of auxiliary mixture sampling for count data and for binary and multinomial data. One of these estimators is based on combiningChib’s estimatorwith data augmentation as in auxiliarymixture sampling,while the other estimators are importance sampling and bridge ...
متن کاملGibbs sampling for fitting finite and infinite Gaussian mixture models
This document gives a high-level summary of the necessary details for implementing collapsed Gibbs sampling for fitting Gaussian mixture models (GMMs) following a Bayesian approach. The document structure is as follows. After notation and reference sections (Sections 2 and 3), the case for sampling the parameters of a finite Gaussian mixture model is described in Section 4. This is then extende...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry B
سال: 2009
ISSN: 1520-6106,1520-5207
DOI: 10.1021/jp808381s