论文标题
用种群退火分子动力学模拟元源吗
Simulating Met-Enkephalin With Population Annealing Molecular Dynamics
论文作者
论文摘要
Met-Enkephalin是最小的鸦片肽之一，并且是重要的神经递质，是分子模拟领域中广泛使用的基准测试问题。通过其可能的低温构象范围通过自由能屏障隔开，以前发现使用直构的分子动力学模拟很难对其进行热效化。在这里，我们演示了如何使用最近提出的人口退火分子动力学方案来克服这些困难。我们展示了如何使用多历一图重新加权，使人们可以准确估计系统状态的密度，从而得出估计值，例如势能（如准温度的准连续功能）。我们进一步研究了自由能的表面，这是端到端距离和半径的函数，并观察到两个不同的吸引力盆地。
Met-enkephalin, one of the smallest opiate peptides and an important neurotransmitter, is a widely used benchmarking problem in the field of molecular simulation. Through its range of possible low-temperature conformations separated by free-energy barriers it was previously found to be hard to thermalize using straight canonical molecular dynamics simulations. Here, we demonstrate how one can use the recently proposed population annealing molecular dynamics scheme to overcome these difficulties. We show how the use of multi-histogram reweighting allows one to accurately estimate the density of states of the system and hence derive estimates such as the potential energy as quasi continuous functions of temperature. We further investigate the free-energy surface as a function of end-to-end distance and radius-of-gyration and observe two distinct basins of attraction.
