dorsal/arxiv
View SchemaOptimized parallel tempering simulations of proteins
| Authors | Simon Trebst, Matthias Troyer, Ulrich H. E. Hansmann |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0602005 |
| URL | https://arxiv.org/abs/q-bio/0602005 |
| DOI | 10.1063/1.2186639 |
| Journal | J. Chem. Phys. 124, 174903 (2006). |
Abstract
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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"abstract": "We apply a recently developed adaptive algorithm that systematically improves\nthe efficiency of parallel tempering or replica exchange methods in the\nnumerical simulation of small proteins. Feedback iterations allow us to\nidentify an optimal set of temperatures/replicas which are found to concentrate\nat the bottlenecks of the simulations. A measure of convergence for the\nequilibration of the parallel tempering algorithm is discussed. We test our\nalgorithm by simulating the 36-residue villin headpiece sub-domain HP-36\nwherewe find a lowest-energy configuration with a root-mean-square-deviation of\nless than 4 Angstroem to the experimentally determined structure.",
"arxiv_id": "q-bio/0602005",
"authors": [
"Simon Trebst",
"Matthias Troyer",
"Ulrich H. E. Hansmann"
],
"categories": [
"q-bio.QM",
"cond-mat.stat-mech",
"physics.comp-ph"
],
"doi": "10.1063/1.2186639",
"journal_ref": "J. Chem. Phys. 124, 174903 (2006).",
"title": "Optimized parallel tempering simulations of proteins",
"url": "https://arxiv.org/abs/q-bio/0602005"
},
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