ArticleJournal of chemical theory and computation2006
A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.
Article in Journal of chemical theory and computation, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
- Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022Review
- Accelerating atomistic simulations of proteins using multiscale enhanced sampling with independent tempering.Journal of computational chemistry · 2021Article
- Health literacy and patient empowerment: separating con-joined twins in the context of chronic low back pain.PloS one · 2015Article
- MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.Chemical physics letters · 2012Article
- Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.The Journal of chemical physics · 2012Article
- Equilibrium sampling in biomolecular simulations.Annual review of biophysics · 2011Review
- Highly polar environments catalyze the unfolding of PrP C helix 1.European biophysics journal : EBJ · 2010Article
- Thermal nanostructure: an order parameter multiscale ensemble approach.The Journal of chemical physics · 2010Article
- Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules.F1000 biology reports · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The replica exchange approach, also called parallel tempering, is gaining popularity for biomolecular simulation. We ask whether the approach is likely to be efficient compared to standard simulation methods for fixed-temperature equilibrium sampling. To examine the issue, we make a number of straightforward observations on how "fast" high-temperature molecular simulations can be expected to run, as well as on how to characterize efficiency in replica exchange. Although our conclusions remain to be fully established, based on a range of results in the literature and some of our own work with a 50-atom peptide, we are not optimistic for the efficiency of replica exchange for canonical sampling of biomolecules.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.