AN ADAPTIVE UMBRELLA SAMPLING PROCEDURE IN CONFORMATIONAL-ANALYSIS USING MOLECULAR-DYNAMICS AND ITS APPLICATION TO GLYCOL
AN ADAPTIVE UMBRELLA SAMPLING PROCEDURE IN CONFORMATIONAL-ANALYSIS USING MOLECULAR-DYNAMICS AND ITS APPLICATION TO GLYCOL
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DOI：
10.1063/1.463947
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发表时间：
1992-11-01
影响因子：
4.4
通讯作者：
KROON, J
中科院分区：
文献类型：
--
作者：
HOOFT, RWW;VANEIJCK, BP;KROON, J
提出了一种利用伞势方法计算分子动力学平均力势的新方法。在模拟过程中，考虑到先前获得的所有结果，定期改进伞势。该方法进行了测试，通过确定的潜在的平均力的中心二面角在乙二醇（作为一个分子在真空中，并在水和四氯化碳的解决方案）。相对于其他方法的优点是，相对少量的人工干预是必要的，并且在小的模拟时间之后的中间结果已经是对平均力的潜力的完整的，尽管是粗略的估计。还提供了一种稳健的方法来估计所获得的构象之间的能量差和平均力（PMF）的潜力的参数的误差。
A novel way has been developed for using the umbrella potential method of calculating the potential of mean force using molecular dynamics. During a simulation, the umbrella potential is improved periodically, taking into account all results obtained previously. The method was tested by the determination of the potential of mean force for the central dihedral angle in glycol (as a molecule in vacuo and in solutions in water and in CCl4). Advantages over other methods are that a relatively small amount of manual intervention is necessary and that an intermediate result after a small simulation time is already a complete, although crude estimate of the potential of mean force. A robust method to estimate the error in obtained energy differences between conformations and in the parameters of the potential of mean force (PMF) is also supplied.