Free-energy calculation via mean-force dynamics using a logarithmic energy landscape
Free-energy calculation via mean-force dynamics using a logarithmic energy landscape
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DOI：
10.1103/physreve.85.066702
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发表时间：
2012-06-11
影响因子：
2.4
通讯作者：
Mikami, Masuhiro
中科院分区：
文献类型：
--
作者：
Morishita, Tetsuya;Itoh, Satoru G.;Mikami, Masuhiro
提出了一种基于平均力动力学(平均力势上的虚拟动力学)的自由能计算方法。该方法利用自由能的对数形式来增强自由能景观上的跨过障碍，从而导致对“罕见”事件的有效采样。引用平均力动力学中的守恒量，自由能可以在不需要后处理的情况下即时估计。这意味着，与基于均力动力学的其他方法(如超动力学)相比，自由能分布的估计可以在局部进行。该方法与传统方法进行了比较，并在甘氨酸二肽分子的自由能计算中得到了验证。
A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule.