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Sampling Free Energy Surfaces as Slices by Combining Umbrella Sampling and Metadynamics

机译:通过结合伞采样将自由能表面取样为切片   和metadynamics

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摘要

Metadynamics (MTD) is a very powerful technique to sample high-dimensionalfree energy landscapes, and due to its self-guiding property, the method hasbeen successful in studying complex reactions and conformational changes. MTDsampling is based on filling the free energy basins by biasing potentials andthus for cases with flat, broad and unbound free energy wells, thecomputational time to sample them becomes very large. To alleviate thisproblem, we combine the standard Umbrella Sampling (US) technique with MTD tosample orthogonal collective variables (CVs) in a simultaneous way. Within thisscheme, we construct the equilibrium distribution of CVs from biaseddistributions obtained from independent MTD simulations with umbrellapotentials. Reweighting is carried out by a procedure that combines USreweighting and Tiwary-Parrinello MTD reweighting within the Weighted HistogramAnalysis Method (WHAM). The approach is ideal for a controlled sampling of a CVin a MTD simulation, making it computationally efficient in sampling flat,broad and unbound free energy surfaces. This technique also allows for adistributed sampling of a high-dimensional free energy surface, furtherincreasing the computational efficiency in sampling. We demonstrate theapplication of this technique in sampling high-dimensional surface for variouschemical reactions using ab initio and QM/MM hybrid molecular dynamicssimulations. Further, in order to carry out MTD bias reweighting for computingforward reaction barriers in ab initio or QM/MM simulations, we propose acomputationally affordable approach that does not require recrossingtrajectories.
机译:Metadynamics(MTD)是一种非常强大的技术,可以对高维自由能态进行采样,并且由于其自导性,该方法已经成功地研究了复杂的反应和构象变化。 MTD采样的基础是通过对势能进行偏置来填充自由能盆,因此对于平坦,宽阔和未约束的自由能井,采样的计算时间变得非常大。为了缓解这个问题,我们将标准的伞式采样(US)技术与MTD相结合,以同时方式对正交集合变量(CV)进行采样。在此方案中,我们从具有伞势的独立MTD模拟获得的偏差分布构造CV的平衡分布。通过在加权直方图分析方法(WHAM)中结合USreweighting和Tiwary-Parrinello MTD reweighting的过程来进行加权。该方法是在MTD模拟中对CV进行受控采样的理想选择,从而使其在对平坦,宽泛和未绑定自由能表面进行采样时计算效率高。该技术还允许对高维自由能表面进行分布式采样,从而进一步提高了采样的计算效率。我们演示了该技术在从头算和QM / MM混合分子动力学模拟中对各种化学反应的高维表面进行采样的应用。此外,为了进行MTD偏差重加权以从头算或QM / MM模拟计算正向反应障碍,我们提出了一种不需要重新交叉轨迹的可算得起的计算方法。

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