论文标题
从AA分子动力学模拟中得出UA分子电位的一种相关方法：应用于烷烃
A Correlation Method for Deriving UA Intra-Molecular Potentials from AA Molecular Dynamics Simulations: Application to Alkanes
论文作者
论文摘要
联合原子（UA）力场通常是根据基于从蒙特卡洛模拟获得的分布来构建的。提出了一种从ALL-AM（AA）分子动力学模拟构建UA力场的新方法。在这种方法中，人们确定了相同类型的振荡器之间的时间相关性：CC键与连接的CH键之间的时间相关；在价角CCC和所有价角之间，与之共享至少一个氢。在二面角CCCC和与之共享两个中央碳的二面角之间。在长度或角度之间无相关性的情况下，振荡器的能量是独立的。在这种情况下，力场的AA和UA组件是相同的。当完全相关时，对象的UA电势是与之耦合的振荡器能量的总和。部分相关也是可能的。 AA分子与相应的UA分子的几个运动学匹配测试被考虑：振荡器的平均振动时间；与存在概率相关的能量；分子的平均端到端长度。例如，该方法用于使用OPLS-AA力场模拟脂肪族分子。
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.
