Free-energy analyses of a proton transfer reaction by simulated-temperingumbrella sampling and first-principles molecular dynamics simulations
Free-energy analyses of a proton transfer reaction by simulated-temperingumbrella sampling and first-principles molecular dynamics simulations
复制标题
通过模拟回火伞采样和第一原理分子动力学模拟对质子转移反应进行自由能分析
DOI：
10.1103/physreve.87.023301
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发表时间：
2013
影响因子：
2.4
通讯作者：
Yuko Okamoto
中科院分区：
文献类型：
--
作者：
Yoshiharu Mori;Yuko Okamoto
本文提出了一种计算化学反应自由能的模拟回火方法，即模拟回火伞取样法。采用第一性原理分子动力学模拟方法研究了水溶液中丙二醛分子内质子转移反应。该方法可以方便地增强反应坐标空间中的构象采样，并能准确地计算沿反应坐标沿着的自由能。此外，模拟回火伞采样提供的轨迹数据比传统的伞采样方法更有效。
A simulated tempering method, which is referred to as simulated-tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed to study the intramolecular proton transfer reaction of malonaldehyde in an aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be calculated accurately. Moreover, the simulated-tempering umbrella sampling provides trajectory data more efficiently than the conventional umbrella sampling method.