Wang-Landau分子动力学技术寻找蛋白质低能构象空间
Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins
摘要：
多正则分子动力学（MD）是一个强大的技术，用于采样构象的崎岖潜在的表面，如蛋白质。然而，它是众所周知的困难，以有效地估计多典型温度。Wang和Landau开发了一种基于多正则蒙特卡罗方法的估算态密度的方便方法。在他们的方法中，态密度是在模拟过程中自主计算的。在本文中，我们开发了一套技术，有效地将王朗道方法MD模拟。在多重正则分子动力学中，态密度导数的估计是关键。为了准确地估计它，我们设计了两个原始的改进。首先，通过使用由短正则模拟获得的高斯分布，使状态密度的校正平滑。其次，应用近似的导数，这是基于高斯分布和多重加权直方图技术。用小分子多肽、Met-脑啡肽和Trp-笼对该方法进行了测试，结果表明Wang-Landau MD与复制交换MD一致，但可以采样更大的构象空间。
英文摘要：
Multicanonical molecular dynamics (MD) is a powerful technique for sampling conformations on rugged potential surfaces such as protein. However, it is notoriously difficult to estimate the multicanonical temperature effectively. Wang and Landau developed a convenient method for estimating the density of states based on a multicanonical Monte Carlo method. In their method, the density of states is calculated autonomously during a simulation. In this paper we develop a set of techniques to effectively apply the Wang-Landau method to MD simulations. In the multicanonical MD, the estimation of the derivative of the density of states is critical. In order to estimate it accurately, we devise two original improvements. First, the correction for the density of states is made smooth by using the Gaussian distribution obtained by a short canonical simulation. Second, an approximation is applied to the derivative, which is based on the Gaussian distribution and the multiple weighted histogram technique. A test of this method was performed with small polypeptides, Met-enkephalin and Trp-cage, and it is demonstrated that Wang-Landau MD is consistent with replica exchange MD but can sample much larger conformational space.
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