期刊
JOURNAL OF CHEMICAL PHYSICS
卷 136, 期 21, 页码 -出版社
AMER INST PHYSICS
DOI: 10.1063/1.4725183
关键词
-
资金
- National Science Foundation (NSF) [CHE 1112067]
- National Science Foundation [TG-CTS090079]
- Center for Computational Molecular Science Technology [CHE 0946869]
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [1112067, 0946869] Funding Source: National Science Foundation
The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD) algorithm [G. Ozer, E. Valeev, S. Quirk, and R. Hernandez, J. Chem. Theory Comput. 6, 3026 (2010)] is used to reproduce the PMF of the unraveling of decaalanine in vacuum by averaging over fewer nonequilibrium trajectories. The efficiency and accuracy of the method are demonstrated through the agreement with the earlier work by Park and Schulten, a series of convergence checks compared to alternate SMD pulling strategies, and an analytical proof. The nonequilibrium trajectories obtained through ASMD have also been used to analyze the intrapeptide hydrogen bonds along the stretching coordinate. As the decaalanine helix is stretched, the initially stabilized i --> i + 4 contacts (alpha-helix) is replaced by i --> i + 3 contacts (3(10)-helix). No significant formation of i --> i + 5 hydrogen bonds (pi-helix) is observed. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4725183]
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据