The Jacobian factor in free energy simulations
The Jacobian factor in free energy simulations
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DOI：
10.1063/1.472358
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发表时间：
1996-09-22
影响因子：
4.4
通讯作者：
Karplus, M
中科院分区：
文献类型：
--
作者：
Boresch, S;Karplus, M
雅可比因子在自由能模拟中的作用。他们提供了一个简单的解释''惯性修正''和''动态拉伸自由能''条款在这样的模拟。由于相关的雅可比因子通常可以通过使用多原子分子的构型配分函数进行分析评估，因此当它们做出非物理贡献时，可以从模拟结果中减去它们。一个重要的情况出现在炼金术模拟中，使用单一拓扑方法，并引入虚拟粒子，使其在初始状态和最终状态下具有相同数量的原子。简要讨论了雅可比因子在复杂系统仿真中的更普遍的应用。(C)1996年美国物理研究所。
The role of Jacobian factors in free energy simulations is described. They provide a simple interpretation of ''moment of inertia correction'' and ''dynamic stretch free energy'' terms in such simulations. Since the relevant Jacobian factors can often be evaluated analytically by use of the configurational partition function of a polyatomic molecule, it is possible to subtract them from the simulation results when they make unphysical contributions. An important case arises in alchemical simulations that use a single topology method and introduce dummy particles to have the same number of atoms in the initial and final state. The more general utility of the Jacobian factors for simulations of complex systems is briefly discussed. (C) 1996 American Institute of Physics.