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...

Full description

Saved in:
Bibliographic Details
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
Tags: Add Tag
No Tags, Be the first to tag this record!
Institution: Nanyang Technological University
Language: English
Description
Summary: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.

Similar Items