Exchange frequency in replica exchange molecular dynamics
Exchange frequency in replica exchange molecular dynamics
复制标题
DOI：
10.1063/1.2816560
复制
发表时间：
2008-01-14
影响因子：
4.4
通讯作者：
Roitberg, Adrian E.
中科院分区：
文献类型：
--
作者：
Sindhikara, Daniel;Meng, Yilin;Roitberg, Adrian E.
在复制交换分子动力学（REMD）中研究了交换尝试频率对采样效率的影响。我们发现，采样效率随着交换尝试频率的增加而增加。这一结论与REMD中普遍表达的观点相反。五个肽（1-21个残基长）的交换尝试率的光谱进行了研究。收敛速度衡量固定长度的测试REMD模拟和更长的参考模拟之间的合奏性能进行比较。为了显示交换频率和收敛时间之间的基本相关性，设计并研究了一个简单的模型，显示了更复杂系统的相同基本行为。(c)2008年美国物理学会。
The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems. (c) 2008 American Institute of Physics.