Optimized parallel tempering simulations of proteins

Details Optimized parallel tempering simulations of proteins Optimized parallel tempering simulations of proteins

2006-02-06

arxiv.org/abs/q-bio/0602005v1

J. Chem. Phys. 124, 174903 (2006).

Biology

Quantitative Biology

Quantitative Methods

22 pages, 7 figures

Scientific paper

10.1063/1.2186639

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 sub-domain HP-36 wherewe find a lowest-energy configuration with a root-mean-square-deviation of less than 4 Angstroem to the experimentally determined structure.

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