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Theory of Adaptive Optimization for Umbrella Sampling
[Image: see text] We present a theory of adaptive optimization for umbrella sampling. With the analytical bias force constant obtained from the constrained thermodynamic length along the reaction coordinate, the windows are distributed to optimize the overlap between neighbors. Combining with the re...
| Autores principales: | , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
American
Chemical Society
2014
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| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089916/ https://www.ncbi.nlm.nih.gov/pubmed/25018672 http://dx.doi.org/10.1021/ct500504g |
| _version_ | 1782325193912352768 |
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| author | Park, Soohyung Im, Wonpil |
| author_facet | Park, Soohyung Im, Wonpil |
| author_sort | Park, Soohyung |
| collection | PubMed |
| description | [Image: see text] We present a theory of adaptive optimization for umbrella sampling. With the analytical bias force constant obtained from the constrained thermodynamic length along the reaction coordinate, the windows are distributed to optimize the overlap between neighbors. Combining with the replica exchange method, we propose a method of adaptive window exchange umbrella sampling. The efficiency gain in sampling by the present method originates from the optimal window distribution, in which windows are concentrated to the region where the free energy is steep, as well as consequently improved random walk. |
| format | Online Article Text |
| id | pubmed-4089916 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2014 |
| publisher | American
Chemical Society |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-40899162015-06-12 Theory of Adaptive Optimization for Umbrella Sampling Park, Soohyung Im, Wonpil J Chem Theory Comput [Image: see text] We present a theory of adaptive optimization for umbrella sampling. With the analytical bias force constant obtained from the constrained thermodynamic length along the reaction coordinate, the windows are distributed to optimize the overlap between neighbors. Combining with the replica exchange method, we propose a method of adaptive window exchange umbrella sampling. The efficiency gain in sampling by the present method originates from the optimal window distribution, in which windows are concentrated to the region where the free energy is steep, as well as consequently improved random walk. American Chemical Society 2014-06-12 2014-07-08 /pmc/articles/PMC4089916/ /pubmed/25018672 http://dx.doi.org/10.1021/ct500504g Text en Copyright © 2014 American Chemical Society Terms of Use (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) |
| spellingShingle | Park, Soohyung Im, Wonpil Theory of Adaptive Optimization for Umbrella Sampling |
| title | Theory
of Adaptive Optimization for Umbrella Sampling |
| title_full | Theory
of Adaptive Optimization for Umbrella Sampling |
| title_fullStr | Theory
of Adaptive Optimization for Umbrella Sampling |
| title_full_unstemmed | Theory
of Adaptive Optimization for Umbrella Sampling |
| title_short | Theory
of Adaptive Optimization for Umbrella Sampling |
| title_sort | theory
of adaptive optimization for umbrella sampling |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4089916/ https://www.ncbi.nlm.nih.gov/pubmed/25018672 http://dx.doi.org/10.1021/ct500504g |
| work_keys_str_mv | AT parksoohyung theoryofadaptiveoptimizationforumbrellasampling AT imwonpil theoryofadaptiveoptimizationforumbrellasampling |