Hamiltonian based resonance-free approach for enabling very large time steps in multiple time-scale molecular dynamics
Hamiltonian based resonance-free approach for enabling very large time steps in multiple time-scale molecular dynamics
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DOI：
10.1080/00268976.2021.1923848
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发表时间：
2021-05
影响因子：
1.7
通讯作者：
C. Abreu;M. Tuckerman
中科院分区：
文献类型：
--
作者：
C. Abreu;M. Tuckerman
扩展的相空间等速方法及其确定性[Minary等人，Phys.莱特牧师。93,150201(2004年)]和随机形式[Leimkuhler等人，Mol.太棒了。111,3579(2013)]在允许以非常大的时间步长执行多时间尺度的分子动力学模拟方面已被证明是非常成功的。这些方法通过等速约束将物理自由度耦合到一组Nosé-Hoover链或Nosé-Hoover Langevin恒温器，从而避免了困扰多个时间步长算法的共振伪影。在本文中，我们介绍了一种新的无共振方法，它在时间步长上获得了相同的增益，但没有施加等速约束或引入扩展的相空间变量。相反，我们修改了物理哈密顿量，该哈密顿量对等动能约束实现的共振进行了相同的调节。在这样做的过程中，我们证明了采样误差是可以控制的，并且可以在更简单的哈密顿框架内改进性能。该方法在液态水结构的模拟以及与增强采样相结合的溶剂化丙氨酸二肽的Ramachandran自由能表面的生成中得到了演示。图形摘要
Extended phase-space isokinetic methods in their deterministic [Minary et al., Phys. Rev. Lett. 93, 150201 (2004)] and stochastic forms [Leimkuhler et al., Mol. Phys. 111, 3579 (2013)] have proved tremendously successful in allowing multiple time-scale molecular dynamics simulations to be performed with very large time steps. These methods work by coupling the physical degrees of freedom to a set of Nosé-Hoover chain or Nosé-Hoover Langevin thermostats via an isokinetic constraint, which has the effect of avoiding resonance artifacts that plague multiple time-step algorithms. In this paper, we introduce a new resonance-free approach that achieves the same gains in time step but without the imposition of isokinetic constraints or the introduction of extended phase-space variables. Rather, we modify the physical Hamiltonian that effects the same regulation of resonances achieved by the isokinetic constraints. In so doing, we show that sampling errors can be controlled and performance improvements are possible within a simpler Hamiltonian framework. The method is demonstrated in simulations of the structure of liquid water and, in conjunction with enhanced sampling, in generation of the Ramachandran free-energy surface of the solvated alanine dipeptide. GRAPHICAL ABSTRACT