Self-healing umbrella sampling: convergence and efficiency
نویسندگان
چکیده
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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Monte Carlo analysis has become nearly ubiquitous since its introduction, now over 65 years ago. It is an important tool in many assessments of the reliability and robustness of systems, structures or solutions. As the deterministic core simulation can be lengthy, the computational costs of Monte Carlo can be a limiting factor. To reduce that computational expense as much as possible, sampling ...
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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 ...
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We present a theory of adaptive optimization for umbrella sampling. With the analytical bias force constant obtained from the constrained thermodynamic length along the reaction coordinate, the windows are distributed to optimize the overlap between neighbors. Combining with the replica exchange method, we propose a method of adaptive window exchange umbrella sampling. The efficiency gain in sa...
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(Received December, 1988) The adaptive umbrella sampling technique, introduced recently to improve the probability ratio method and found to perform more reliably then the customary harmonic umbrella sampling, is tested and compared with other free energy methods. One of the tests applies the method to a transition involving a chemical change: calculation of the hydration free energy difference...
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ژورنال
عنوان ژورنال: Statistics and Computing
سال: 2015
ISSN: 0960-3174,1573-1375
DOI: 10.1007/s11222-015-9613-2