Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions
Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions
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DOI：
10.1063/1.2913050
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发表时间：
2008-05-07
影响因子：
4.4
通讯作者：
van Gunsteren, Wilfred F.
中科院分区：
文献类型：
--
作者：
Christ, Clara D.;van Gunsteren, Wilfred F.
最近提出的从参考状态的单个模拟获得多个端态的自由能差的方法被称为包络分布采样（EDS）[J. Chem. Phys. 126，184 - 110（2007）]，该方法被扩展到端态构型空间密度不显示重叠的情况。它使用Han在1992年提出的参考态哈密顿量[Phys. Lett. A 165，28（1992）]中。该方法使我们能够计算多个自由能差异“在飞”从一个单一的分子动力学模拟。研究了各参数对自由能差的准确度和精度的影响。建立了所提出的方法和班尼特接受比方法之间的联系。该方法适用于四个两态测试系统（偶极反转，货车德瓦尔斯扰动，电荷反转，和水到甲醇的转换）和两个多态测试系统[偶极反转与五个充电状态和五个（消失）出现的水分子]。如果参考态哈密顿量的参数按照给定的算法进行优化，则对于所有的测试应用都可以得到准确的结果。与精确结果或独立计算的偏差至多为0.6 kJ/mol。自由能差的精确估计总是可能的，与端态的不同程度无关。然而，自由能差的收敛时间在端态构型空间密度不显示重叠的情况下[电荷反转，水到甲醇的转化，（消失）出现的水分子]比在构型空间密度确实显示一些重叠的情况下[（多个）偶极反转和货车德瓦尔斯扰动]更长。(C)2008年美国物理学会。
A recently proposed method to obtain free energy differences for multiple end states from a single simulation of a reference state which was called enveloping distribution sampling (EDS) [J. Chem. Phys. 126, 184110 (2007)] is expanded to situations where the end state configuration space densities do not show overlap. It uses a reference state Hamiltonian suggested by Han in 1992 [Phys. Lett. A 165, 28 (1992)] in a molecular dynamics implementation. The method allows us to calculate multiple free energy differences "on the fly" from a single molecular dynamics simulation. The influence of the parameters on the accuracy and precision of the obtained free energy differences is investigated. A connection is established between the presented method and the Bennett acceptance ratio method. The method is applied to four two-state test systems (dipole inversion, van der Waals perturbation, charge inversion, and water to methanol conversion) and two multiple-state test systems [dipole inversion with five charging states and five (dis-)appearing water molecules]. Accurate results could be obtained-for all test applications if the parameters of the reference state Hamiltonian were optimized according to a given algorithm. The deviations from the exact result or from an independent calculation were at most 0.6 kJ/mol. An accurate estimation of the free energy difference is always possible, independent of how different the end states are. However, the convergence times of the free energy differences are longer in cases where the end state configuration space densities do not show overlap [charge inversion, water to methanol conversion, (dis-)appearing water molecules] than in cases where the configuration space densities do show some overlap [(multiple) dipole inversion and van der Waals perturbation]. (C) 2008 American Institute of Physics.