From Metadynamics to Dynamics
From Metadynamics to Dynamics
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DOI：
10.1103/physrevlett.111.230602
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发表时间：
2013-12-03
影响因子：
8.6
通讯作者：
Parrinello, Michele
中科院分区：
文献类型：
--
作者：
Tiwary, Pratyush;Parrinello, Michele
代谢动力学是一种常用且成功的增强采样方法。通过引入依赖于有限数量的集体变量的历史依赖性偏置，它可以探索复杂的自由能表面，其特征在于由几个亚稳态分离的大的自由能势垒。在这里，我们通过引入一个简单而强大的方法来计算不同亚稳态之间的过渡率，从而扩展了它的范围。该方法不依赖于过渡态或反应坐标的先前知识，只要已知可以区分自由能空间中的各种稳定最小值的集体变量。我们证明，我们的方法恢复正确的逃逸率出这些稳定的状态，也保留了正确的序列的状态到状态的转换，与普通的元自适应需要最小的额外的计算工作。我们适用于三个不同的问题的形式主义，并在每种情况下找到很好的协议与长期无偏分子动力学运行的结果。
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased molecular dynamics runs.