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Simulating rare events using a weighted ensemble-based string method

机译:使用基于加权合奏的字符串方法模拟罕见事件

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摘要

We introduce an extension to the weighted ensemble (WE) path sampling method to restrict sampling to a one-dimensional path through a high dimensional phase space. Our method, which is based on the finite-temperature string method, permits efficient sampling of both equilibrium and non-equilibrium systems. Sampling obtained from the WE method guides the adaptive refinement of a Voronoi tessellation of order parameter space, whose generating points, upon convergence, coincide with the principle reaction pathway. We demonstrate the application of this method to several simple, two-dimensional models of driven Brownian motion and to the conformational change of the nitrogen regulatory protein C receiver domain using an elastic network model. The simplicity of the two-dimensional models allows us to directly compare the efficiency of the WE method to conventional brute force simulations and other path sampling algorithms, while the example of protein conformational change demonstrates how the method can be used to efficiently study transitions in the space of many collective variables.
机译:我们引入了加权集成(WE)路径采样方法的扩展,以将采样限制为通过高维相空间的一维路径。我们的方法基于有限温度串方法,可以对平衡和非平衡系统进行有效采样。从WE方法获得的采样指导对阶数参数空间的Voronoi细分进行自适应细化,其收敛时的生成点与主要反应路径一致。我们展示了该方法在驱动布朗运动的几个简单的二维模型以及使用弹性网络模型的氮调节蛋白C受体域构象变化中的应用。二维模型的简单性使我们可以直接将WE方法的效率与传统的蛮力模拟和其他路径采样算法进行比较,而蛋白质构象变化的示例说明了如何使用该方法有效地研究WE中的过渡。许多集体变量的空间。

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