Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy
Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy
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DOI：
10.1021/jp972280j
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发表时间：
1998-01-29
影响因子：
3.3
通讯作者：
Karplus, M
中科院分区：
文献类型：
--
作者：
Bartels, C;Karplus, M
提出了一种基于势能的自适应伞形采样分子动力学算法，以减少推导分子体系平衡性质所需的模拟时间。势能，在通常使用的伞势相反，是特别感兴趣的复杂系统，因为它不依赖于假设的几何形状，也不对知识的重要构象和过渡态，参与平衡。该方法通过将其应用于苏氨酸二肽和甲硫氨酸脑啡肽来说明。对于苏氨酸二肽，从一个单一的10 ns的运行，来自系统的所有二面角的平均力的潜力。通过与以前的结果进行比较，证实了潜力的准确性。甲硫氨酸脑啡肽在300 K时有几种不同的构象。三个代表性的结构被用来聚类的优势构象。计算了二面角的平衡分布和两个端点之间的距离。分析了结果的精度，并讨论了所提出的自适应伞形采样方法的实用性。
An adaptive umbrella sampling molecular dynamics algorithm based on the potential energy is introduced to reduce the simulation time required for deriving equilibrium properties of molecular systems. The potential energy, in contrast to the commonly used umbrella potentials, is of particular interest for complex systems because it does not depend on assumptions about the geometry nor on a knowledge of the important conformations and transition states that are involved in the equilibration. The method is illustrated by applying it to the threonine dipeptide and to met-Enkephalin. For the threonine dipeptide, potentials of mean force for all dihedral angles of the system are derived from a single 10 ns run. The accuracy of the potentials is confirmed by comparison with previous results. Met-Enkephalin is found to sample several different conformations at 300 K. Three representative structures are used to cluster the dominant conformations. Equilibrium distributions of dihedral angles and the distance between the two termini are calculated. The precision of the results is analyzed, and the utility of the proposed adaptive umbrella sampling method is discussed.