The role of bonded terms in free energy simulations. 2. Calculation of their influence on free energy differences of solvation
The role of bonded terms in free energy simulations. 2. Calculation of their influence on free energy differences of solvation
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DOI：
10.1021/jp981629f
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发表时间：
1999-01-07
影响因子：
2.9
通讯作者：
Karplus, M
中科院分区：
文献类型：
--
作者：
Boresch, S;Karplus, M
利用溶剂化自由能差的计算，研究了力场中键伸缩和角弯曲能项的化学变化所产生的贡献。这些结果说明了在伴文(Boresch，S.；Karplus，M.)中对这些项的理论分析。自由能模拟中键项的作用：1.理论分析。J.Phys.化学。A 1998、103、103(10))。研究了三个模型体系：(A)两个一维谐振子与代表溶剂的第三粒子的相互作用；(B)两个双原子分子的水溶剂化；(C)乙烷和甲醇的水溶剂化。在每种情况下，都使用单拓扑和双拓扑方法进行计算。通过比较计算中得到的单自由能差和双自由能差的自由能分量，可以确定理论分析所涉及的三个贡献，即振动PMF型项和雅可比因子项。通过实例对理论分析进行了验证，为解决所谓的自项能否对双自由能差做出重大贡献这一问题提供了依据。这是通过确定来自键能项的三个贡献的耦合对双自由能差的影响来实现的。对于所研究的模型系统，耦合以及自项被发现是不重要的。这种分析解决了文献中关于这一问题的模棱两可的问题。
Calculations of the free energy difference of solvation are used to study the contributions arising from alchemical changes of bond stretching and angle bending energy terms in the force field. The results illustrate the theoretical analysis of such terms given in the companion paper (Boresch, S.; Karplus, M. The Role of Bonded Terms in Free Energy Simulations: 1. Theoretical Analysis. J. Phys. Chem. A 1998, 103, 103(10)). Three model systems are investigated: (a) two one-dimensional harmonic oscillators interacting with a third particle that represents the solvent, (b) the aqueous solvation of two diatomic molecules, and (c) the aqueous solvation of ethane and methanol. In each case, the computations are carried out with both a single topology and a dual topology methodology. A comparison of free energy components of the single and double free energy differences obtained in the calculations makes it possible to identify the three contributions that the theoretical analysis showed were involved, i.e., vibrational pmf-type, and Jacobian factor terms. The verification of the theoretical analysis by illustrative examples provides the basis for addressing the question of whether the so-called self-terms can make significant contributions to double free energy differences. This is accomplished by identifying the effect of coupling of the three contributions from bonded energy terms on a double free energy difference. For the model systems studied, coupling and, hence, self-terms are found to be of little importance. The analysis resolves the ambiguities concerning this issue in the literature.