使用哈密顿量副本交换增强的单参考热力学积分计算溶剂化的相对自由能。
Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.
作者信息
Khavrutskii Ilja V, Wallqvist Anders
机构信息
Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702.
出版信息
J Chem Theory Comput. 2010 Nov 9;6(11):3427-3441. doi: 10.1021/ct1003302.
Abstract
This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.
摘要
本文介绍了一种高效的热力学积分（TI）单拓扑变体，用于计算一系列分子相对于单个参考态的相对转化自由能。我们将提出的TI变体称为单参考TI（SR-TI），它将成熟的分子模拟方法整合为一种实用的计算工具。通过哈密顿量副本交换（HREX）增强后，SR-TI变体可以在选定的自由度上实现增强采样。在计算一系列复杂度不断增加的苯衍生物的相对溶剂化自由能时，展示了SR-TI变体的实用性。值得注意的是，带有HREX选项的SR-TI变体在一个具有高（13-15千卡/摩尔）内顺/反互变势垒的酰胺分子的具有挑战性的案例中，仅使用1至4纳秒的模拟时间就提供了收敛结果。
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