Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment
Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment
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DOI：
10.1063/1.2908251
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发表时间：
2008-05-28
影响因子：
4.4
通讯作者：
Pande, Vijay S.
中科院分区：
文献类型：
--
作者：
Huang, Xuhui;Bowman, Gregory R.;Pande, Vijay S.
我们在全球分布式计算环境中实现了串行副本交换方法（SREM）和模拟回火（ST）增强采样算法。在这里，我们研究了21残基α -螺旋肽在显式溶剂中的螺旋-线圈转变。对于ST，我们证明了一种确定初始权重的新方法的有效性，该方法允许系统在基于短试验模拟的温度空间中进行随机漫步。通过自适应加权方法在整个生产模拟过程中更新这些权重。我们对SREM、ST和标准MD进行了详细的比较，发现SREM和ST给出了与实验数据相当的结果。此外，我们发现两种增强的采样方法都比标准MD模拟有效得多。计算得到具有AMBER99 phi电位的Fs肽的熔化温度约为310 K，与实验值334 K基本吻合。我们还讨论了螺旋-线圈转变的其他温度相关性质。虽然ST比SREM有一定的优势，但SREM和ST都是通过分布式计算被证明是强大的方法，将在未来复杂生物分子系统的研究中得到广泛应用。(C) 2008年美国物理研究所。
e have implemented the serial replica exchange method (SREM) and simulated tempering (ST) enhanced sampling algorithms in a global distributed computing environment. Here we examine the helix-coil transition of a 21 residue alpha-helical peptide in explicit solvent. For ST, we demonstrate the efficacy of a new method for determining initial weights allowing the system to perform a random walk in temperature space based on short trial simulations. These weights are updated throughout the production simulation by an adaptive weighting method. We give a detailed comparison of SREM, ST, as well as standard MD and find that SREM and ST give equivalent results in reasonable agreement with experimental data. In addition, we find that both enhanced sampling methods are much more efficient than standard MD simulations. The melting temperature of the Fs peptide with the AMBER99 phi potential was calculated to be about 310 K, which is in reasonable agreement with the experimental value of 334 K. We also discuss other temperature dependent properties of the helix-coil transition. Although ST has certain advantages over SREM, both SREM and ST are shown to be powerful methods via distributed computing and will be applied extensively in future studies of complex bimolecular systems. (C) 2008 American Institute of Physics.