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On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

机译:从头算模拟中使用加速的分子动力学来增强结构采样

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摘要

We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. >2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 105, while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H2O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na−Cl in water, accelerating the convergence by a factor of ∼3−4 compared to conventional AIMD simulations.() These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment.
机译:我们已经在从头算MD的框架内实施了加速分子动力学方法(Hamelberg,D。; Mongan,J。; McCammon,JAJ Chem。Phys。> 2004 ,120(24),11919)。 AIMD)。通过三个简单的例子,我们证明了加速AIMD(A-AIMD)可用于加速AIMD模拟中的溶剂弛豫并促进反应坐标的检测:(i)对于气相中的一个环己烷分子,我们证明了该方法可用于将椅子到椅子的相互转换速率提高约1×10 5 ,同时可以重建低能态的正确规范分布。 (ii)然后,对于64个H2O分子的水箱,我们证明A-AIMD也可以在缩合相中用于加速水构象的采样,而不会影响溶剂的结构特性; (iii)然后将该方法用于计算Na-Cl在水中解离的平均力(PMF)的潜力,与传统的AIMD模拟相比,将收敛速度提高了约3-4倍。提示A-AIMD是现有方法的有用补充,用于增强溶液中的构象和相空间采样。尽管该方法不会多余地使用集体变量,但它也不需要用户定义一组集体变量,这些变量可以捕获势能表面上的所有低能极小值。当处理需要量子力学处理的高度复杂的多维系统时,此属性可能非常有用。

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