Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency,Journal of Computational Chemistry

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Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2022-11-08 , DOI: 10.1002/jcc.27020
Daiki Fukuhara _{1,

2} , Masataka Yamauchi _{1,

2} , Satoru G Itoh _{1,

2,

3} , Hisashi Okumura _{1,

2,

3}

Affiliation

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.

中文翻译：

巧妙地执行副本排列：如何对状态标签进行排序以提高采样效率

在副本置换方法中，副本交换方法的高级版本，参数置换考虑了副本和参数的所有组合，并准备了所有组合的列表。在这里，我们报告温度转变概率取决于列表的创建方式，尤其是在具有溶质回火的复制排列 (RPST) 中。我们发现，当组合按顺序分配给最初提出的列表中的状态标签时，大型副本索引的转移概率会降低。为了解决这个问题，我们建议通过将组合随机分配给状态标签来修改列表。我们使用具有“随机分配”列表 (RPST-RA) 的 RPST 和具有“顺序分配”列表 (RPST-SA) 的 RPST 对淀粉样蛋白-β(16–22) 肽进行了分子动力学模拟。

更新日期：2022-11-08

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