ArticleChemical physics letters2012
MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.
Article in Chemical physics letters, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
4 citing papers in PubMed.
- Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.The journal of physical chemistry. B · 2016Article
- Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.The Journal of chemical physics · 2016Article
- Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.Journal of computational chemistry · 2015Article
- Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.Journal of chemical theory and computation · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Replica exchange methods have become popular tools to explore conformational space for small proteins. For larger biological systems, even with enhanced sampling methods, exploring the free energy landscape remains computationally challenging. This problem has led to the development of many improved replica exchange methods. Unfortunately, testing these methods remains expensive. We propose a Molecular Dynamics Meta-Simulator (MDMS) based on transition state theory to simulate a replica exchange simulation, eliminating the need to run explicit dynamics between exchange attempts. MDMS simulations allow for rapid testing of new replica exchange based methods, greatly reducing the amount of time needed for new method development.
Identifiers
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Registered trials
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