Optimized parallel tempering simulations of proteins

被引：193

作者：

Trebst, S ^{[1
]}

Troyer, M

Hansmann, UHE

机构：

[1] ETH, Comp Lab, CH-8092 Zurich, Switzerland

[2] ETH, Theoret Phys, CH-8093 Zurich, Switzerland

[3] Univ Calif Santa Barbara, Microsoft Res & Kavli Inst Theoret Phys, Santa Barbara, CA 93106 USA

[4] Michigan Technol Univ, Dept Phys, Houghton, MI 49931 USA

[5] Forschungszentrum Julich, John von Heumann Inst Comp, D-52425 Julich, Germany

来源：

JOURNAL OF CHEMICAL PHYSICS | 2006年 / 124卷 / 17期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1063/1.2186639

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an optimal set of temperatures/replicas which are found to concentrate at the bottlenecks of the simulations. A measure of convergence for the equilibration of the parallel tempering algorithm is discussed. We test our algorithm by simulating the 36-residue villin headpiece subdomain HP-36 where we find a lowest-energy configuration with a root-mean-square deviation of less than 4 A to the experimentally determined structure.

引用

页数：6

共 27 条

[1] Performance limitations of flat-histogram methods -: art. no. 097201 [J].