The role of bonded energy terms in free energy simulations - Insights from analytical results
The role of bonded energy terms in free energy simulations - Insights from analytical results
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DOI：
10.1080/08927020211969
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发表时间：
2002-01-01
影响因子：
2.1
通讯作者：
Boresch, S
中科院分区：
文献类型：
--
作者：
Boresch, S
统计力学分析的作用，键拉伸和角度弯曲的条款，以及虚拟原子，在炼金术的自由能模拟。它允许一个解决几个模糊的关于他们的待遇从第一原则。的相对重要性的振动，雅可比因子和潜在的平均力的贡献，从键合能项，以单，双自由能差进行比较。对于虚原子，可以得出另外的结论。特别是，它表明，在热力学循环计算中获得的双自由能差总是可以独立的虚拟原子的治疗。此外，在这样的应用中的单和双拓扑计算的等效性被证明。理论上的考虑是伴随着，并说明了异丁烷和丙烷之间的溶剂化的自由能差的模拟结果。
A statistical mechanical analysis of the role of bond stretching and angle bending terms, as well as of dummy atoms, in alchemical free energy simulations is presented. It allows one to resolve several ambiguities concerning their treatment from first principles. The relative importance of vibrational, Jacobian factor and potential-of-mean-force-like contributions from bonded energy terms to single and dual free energy differences is compared. Additional conclusions can be drawn for dummy atoms. In particular, it is shown that double free energy differences obtained in thermodynamic cycle calculations can always be made independent of the treatment of dummy atoms. Further, the equivalence of single and dual topology calculations in such applications is demonstrated. The theoretical considerations are accompanied and illustrated by simulation results for the free energy difference of solvation between iso-butane and propane.