Optimization of replica exchange temperature ladder under the well-tempered ensemble

Optimization of replica exchange temperature ladder under the well-tempered ensemble

Selection of temperature sequence and bias factor is a critical step for the preparation of Parallel Tempering simulations in a Well-Tempered Ensemble (PT-WTE). We provide a scheme in this study to generate the temperature sequence and the corresponding bias factor optimally. The number of replicas...

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Main Authors: Liu, Yang, Li, Weifeng, Mu, Yuguang
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2020
Subjects:
Science::Biological sciences
PT-WTE
Temperature Sequence Optimization
Online Access:https://hdl.handle.net/10356/136890
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-1368902023-02-28T17:06:16Z Optimization of replica exchange temperature ladder under the well-tempered ensemble Liu, Yang Li, Weifeng Mu, Yuguang School of Biological Sciences Science::Biological sciences PT-WTE Temperature Sequence Optimization Selection of temperature sequence and bias factor is a critical step for the preparation of Parallel Tempering simulations in a Well-Tempered Ensemble (PT-WTE). We provide a scheme in this study to generate the temperature sequence and the corresponding bias factor optimally. The number of replicas for a complete coverage of a specific temperature range is adjustable in this scheme, while keeping the average acceptance probability (AAP) between neighboring replica-pairs unchanged. Two series of PT-WTE simulations were tested with the number of replicas as 16 and 8 respectively. This work leads to a better understanding and application of PT-WTE simulations. MOE (Min. of Education, S’pore) NMRC (Natl Medical Research Council, S’pore) MOH (Min. of Health, S’pore) Accepted version 2020-02-04T08:09:48Z 2020-02-04T08:09:48Z 2018 Journal Article Liu, Y., Li, W., & Mu, Y. (2018). Optimization of replica exchange temperature ladder under the well-tempered ensemble. Chemical Physics Letters, 711, 66-72. doi:10.1016/j.cplett.2018.09.036 0009-2614 https://hdl.handle.net/10356/136890 10.1016/j.cplett.2018.09.036 2-s2.0-85053426920 711 66 72 en Chemical Physics Letters © 2018 Elsevier B.V. All rights reserved. This paper was published in Chemical Physics Letters and is made available with permission of Elsevier B.V. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Science::Biological sciences
PT-WTE
Temperature Sequence Optimization
spellingShingle Science::Biological sciences
PT-WTE
Temperature Sequence Optimization
Liu, Yang
Li, Weifeng
Mu, Yuguang
Optimization of replica exchange temperature ladder under the well-tempered ensemble
description Selection of temperature sequence and bias factor is a critical step for the preparation of Parallel Tempering simulations in a Well-Tempered Ensemble (PT-WTE). We provide a scheme in this study to generate the temperature sequence and the corresponding bias factor optimally. The number of replicas for a complete coverage of a specific temperature range is adjustable in this scheme, while keeping the average acceptance probability (AAP) between neighboring replica-pairs unchanged. Two series of PT-WTE simulations were tested with the number of replicas as 16 and 8 respectively. This work leads to a better understanding and application of PT-WTE simulations.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Liu, Yang
Li, Weifeng
Mu, Yuguang
format Article
author Liu, Yang
Li, Weifeng
Mu, Yuguang
author_sort Liu, Yang
title Optimization of replica exchange temperature ladder under the well-tempered ensemble
title_short Optimization of replica exchange temperature ladder under the well-tempered ensemble
title_full Optimization of replica exchange temperature ladder under the well-tempered ensemble
title_fullStr Optimization of replica exchange temperature ladder under the well-tempered ensemble
title_full_unstemmed Optimization of replica exchange temperature ladder under the well-tempered ensemble
title_sort optimization of replica exchange temperature ladder under the well-tempered ensemble
publishDate 2020
url https://hdl.handle.net/10356/136890
_version_ 1759857391034171392

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