Optimized parallel tempering simulations of proteins
نویسندگان
چکیده
منابع مشابه
Optimized parallel tempering simulations of proteins.
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 pa...
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We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins...
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In this work we consider a criterion for selecting temperature intervals in parallel-tempering molecular simulations. Parallel tempering sor replica exchanged is a technique used to enhance the sampling of configurations. The primary aim is to enable systems being simulated at low temperatures to overcome energetic barriers that hinder their sampling and sometimes lead to nonergodicities. The e...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2006
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.2186639