Eigenvector method for umbrella sampling enables error analysis
نویسندگان
چکیده
منابع مشابه
Eigenvector method for umbrella sampling enables error analysis.
Umbrella sampling efficiently yields equilibrium averages that depend on exploring rare states of a model by biasing simulations to windows of coordinate values and then combining the resulting data with physical weighting. Here, we introduce a mathematical framework that casts the step of combining the data as an eigenproblem. The advantage to this approach is that it facilitates error analysi...
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Umbrella sampling simulations, or biased molecular dynamics, can be used to calculate the free-energy change of a chemical reaction. We investigate the sources of different sampling errors and derive approximate expressions for the statistical errors when using harmonic restraints and umbrella integration analysis. This leads to generally applicable rules for the choice of the bias potential an...
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متن کاملBridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration".
We present a method to analyze biased molecular-dynamics and Monte Carlo simulations, also known as umbrella sampling. In the limiting case of a strong bias, this method is equivalent to thermodynamic integration. It employs only quantities with easily controllable equilibration and greatly reduces the statistical errors compared to the standard weighted histogram analysis method. We show the s...
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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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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2016
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.4960649