用群体退火分子动力学模拟甲硫氨酸脑啡肽
Simulating Met-Enkephalin With Population Annealing Molecular Dynamics
摘要：
甲硫氨酸脑啡肽是最小的阿片肽之一，也是重要的神经递质，是分子模拟领域中广泛应用的基准问题。通过它的范围内可能的低温构象分离的自由能障碍，它以前被发现是很难热化使用直正则分子动力学模拟。在这里，我们演示了如何可以使用最近提出的人口退火分子动力学计划，以克服这些困难。我们展示了如何使用多直方图重新加权允许一个准确地估计系统的状态密度，从而获得估计，如准连续函数的温度的势能。我们进一步研究了自由能表面作为端到端的距离和半径的回转的函数，并观察到两个不同的盆地的吸引力。
英文摘要：
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.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
