ArticleJournal of computational chemistry2023
Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.
Article in Journal of computational chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Why Is Arginine the Only Amino Acid That Inhibits Polyglutamine Monomers from Taking on Toxic Conformations?ACS chemical neuroscience · 2024Article
- Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.Journal of computational chemistry · 2023Article
- Article
- Inhibition of amyloid-β(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation.Biophysics and physicobiology · 2023Article
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Authors and funding
4 authors.
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Abstract
In the replica-permutation method, an advanced version of the replica-exchange method, all combinations of replicas and parameters are considered for parameter permutation, and a list of all the combinations is prepared. Here, we report that the temperature transition probability depends on how the list is created, especially in replica permutation with solute tempering (RPST). We found that the transition probabilities decrease at large replica indices when the combinations are sequentially assigned to the state labels as in the originally proposed list. To solve this problem, we propose to modify the list by randomly assigning the combinations to the state labels. We performed molecular dynamics simulations of amyloid-β(16-22) peptides using RPST with the "randomly assigned" list (RPST-RA) and RPST with the "sequentially assigned" list (RPST-SA). The results show the decreases in the transition probabilities in RPST-SA are eliminated, and the sampling efficiency is improved in RPST-RA.
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