This title appears in the Scientific Report :
2006
Please use the identifier:
http://dx.doi.org/10.1063/1.2186639 in citations.
Please use the identifier: http://hdl.handle.net/2128/2371 in citations.
Optimized parallel tempering simulations of proteins
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 concentrat...
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Personal Name(s): | Trebst, S. |
---|---|
Troyer, M. / Hansmann, U. H. E. | |
Contributing Institute: |
John von Neumann - Institut für Computing; NIC |
Published in: | The @journal of chemical physics, 124 (2006) S. 174903 |
Imprint: |
Melville, NY
American Institute of Physics
2006
|
Physical Description: |
174903 |
PubMed ID: |
16689600 |
DOI: |
10.1063/1.2186639 |
Document Type: |
Journal Article |
Research Program: |
Scientific Computing |
Series Title: |
Journal of Chemical Physics
124 |
Subject (ZB): | |
Link: |
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Publikationsportal JuSER |
Please use the identifier: http://hdl.handle.net/2128/2371 in citations.
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. |