从AA分子动力学模拟推导UA分子内势的关联方法：烷烃的应用
A Correlation Method for Deriving UA Intra-Molecular Potentials from AA Molecular Dynamics Simulations: Application to Alkanes
摘要：
联合原子（UA）力场通常使用基于蒙特卡罗模拟获得的分布的玻尔兹曼逆方法来构造。提出了一种利用全原子（AA）分子动力学模拟构造UA力场的新方法。在这种方法中，我们确定了同一类型振子之间的时间相关性：CC键与所连接的CH键之间的时间相关性;价角CCC与所有与它共享至少一个氢的价角之间的时间相关性;二面角CCCC与它共享两个中心碳的二面角之间的时间相关性。在这种情况下，力场的AA和UA分量是相同的。当关联是全关联时，一个物体的UA势是耦合到它的振子的能量之和。部分关联也是可能的。几个运动学匹配测试的AA分子与相应的UA分子被认为是：平均周期的振荡器的振动;与存在概率相关的能量;平均端到端的长度的分子。该方法是，作为一个例子，适用于脂肪族分子，模拟与OPLS-AA力场。
英文摘要：
United-Atom (UA) force fields are usually constructed using a Boltzmann-inverse method based on distributions obtained from Monte-Carlo simulations. A new method of constructing UA force fields from All-Atom (AA) molecular dynamics simulations is proposed. In this method, one determines time correlations between oscillators of the same type: between a CC bond and the connected CH bonds; between a valence angle CCC and all valence angles sharing at least one hydrogen with it; between a dihedral angle CCCC and the dihedral angles sharing the two central carbons with it. In the case of no correlation between lengths or angles, energies of the oscillators are independent. In this case, the AA and UA components of the force fields are identical. When a correlation is total, the UA potential of an object is the sum of the energies of the oscillators coupled to it. Partial correlations are also possible. Several kinematic matching tests of the AA molecule with the corresponding UA molecule are considered: mean periods of vibration of the oscillators; energies associated with presence probabilities; mean end-to-end lengths of the molecules. The method is, as an example, applied to aliphatic molecules, simulated with the OPLS-AA force field.
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