Communication: Multicanonical entropy-like solution of statistical temperature weighted histogram analysis method
نویسندگان
چکیده
منابع مشابه
Temperature weighted histogram analysis method, replica exchange, and transition paths.
We analyzed the data from a replica exchange molecular dynamics simulation using the weighted histogram analysis method to combine data from all of the temperature replicas (T-WHAM) to obtain the room-temperature potential of mean force of the G-peptide (the C-terminal beta-hairpin of the B1 domain of protein G) in regions of conformational space not sampled at room temperature. We were able to...
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There are situations in which it is necessary to combine samples obtained under different simulation conditions to determine properties (e.g. averages or PMFs) of the system under a single condition (which may not even be one of the conditions that were actually simulated). One example is the determination of a PMF to obtain accurate measures of a free energy barrier. If the barrier is substant...
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We present an iteration-free weighted histogram method in terms of intensive variables that directly determines the inverse statistical temperature, β(S) = ∂S/∂E, with S the microcanonical entropy. The method eliminates iterative evaluations of the partition functions intrinsic to the conventional approach and leads to a dramatic acceleration of the posterior analysis of combining statistically...
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The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen’s Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The method is presented here as an extension of the Umbrella Sampling method for free-energy and Potential of Mean Force calculations. This algorithm possesses the following advantages over methods that a...
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We consider the minimization over probability measures of the expected value of a random variable, regularized by relative entropy with respect to a given probability distribution. In the general setting we provide a complete characterization of the situations in which a finite optimal value exists and the situations in which a minimizing probability distribution exists. Specializing to the cas...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2011
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.3651627