Free energy barriers from biased molecular dynamics simulations
Free energy barriers from biased molecular dynamics simulations
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DOI：
10.1063/5.0020240
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发表时间：
2020-09-21
影响因子：
4.4
通讯作者：
Neyts, Erik C.
中科院分区：
文献类型：
--
作者：
Bal, Kristof M.;Fukuhara, Satoru;Neyts, Erik C.
用于自由能定量的原子模拟方法被广泛使用。这些方法通过沿着一小组合适的集体变量（CV）对系统的概率密度进行采样来操作，而集体变量又以自由能表面（FES）的形式表示。这个定义的FES可以捕获的亚稳态的相对稳定性，但不是过渡态，因为势垒高度是不恒定的CV的选择。因此，自由能垒不能一致地计算从FES。在这里，我们提出了一个简单的方法来计算必要的规范修正，以消除这种不一致性。使用我们的程序，标准的FES，以及其规范校正对应的可以通过重新称重相同的模拟轨迹，在很少的额外费用。我们将该方法应用到一些系统中的粒子溶剂化的Lennard-Jones流体，狄尔斯-阿尔德反应，和结晶的液体钠，以证明其能够产生一致的自由能垒，正确地捕获化学或物理转化的动力学，并讨论它提出的额外要求上选择的CV。由于FES可以在相对短的时间尺度（亚纳秒）收敛，基于自由能的反应动力学描述是一个特别有吸引力的选择，以研究化学过程在更昂贵的量子力学理论水平。
Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems-a particle solvated in a Lennard-Jones fluid, a Diels-Alder reaction, and crystallization of liquid sodium-to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory.