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Biased Metropolis Sampling for Rugged Free Energy Landscapes

机译:偏离大都市对坚固的自由能景观的抽样

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Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which uses probability densities from a higher temperature to improve the algorithmic performance at a lower temperature. The method is suitable for canonical as well as for generalized ensemble simulations. A simple approximation to the full transformation is tested at room temperature for Met-Enkephalin in vacuum. Integrated autocorrelation times are found to be reduced by factors close to two and a similar improvement due to generalized ensemble methods enters multiplicatively.
机译:考虑了肽(即小蛋白质)的全原子模型的大都市模拟。灵感来自Bryngelson的漏斗图片和弱,定义了二面角的更新概率的转变,其使用较高温度的概率密度来提高较低温度的算法性能。该方法适用于规范和广义集合模拟。在真空中在室温下测试到完全转化的简单近似。发现综合自相关时间通过接近的两个因素减少,并且由于广义集合方法引起的类似改进进入倍增。

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