Replica exchange molecular dynamics (REMD) simulation is a popular enhanced sampling method that is widely used for exploring the atomic mechanism of protein conformational change. However, the requirement of huge computational resources for REMD, especially with the explicit solvent model, largely limits its application. In this study, the availability and efficiency of a variant of velocity-scaling REMD (vsREMD) was assessed with adenylate kinase as an example. Although vsREMD achieved results consistent with those from conventional REMD and experimental studies, the number of replicas required for vsREMD (30) was much less than that for conventional REMD (80) to achieve a similar acceptance rate (∼0.2), demonstrating high efficiency of vsREMD to characterize the protein conformational change and associated free-energy profile. Thus, vsREMD is a highly efficient approach for studying the large-scale conformational change of protein systems.

中文翻译：

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通过复制交换分子动力学模拟探索腺苷酸激酶的构象变化

副本交换分子动力学 (REMD) 模拟是一种流行的增强采样方法，广泛用于探索蛋白质构象变化的原子机制。然而，REMD 对大量计算资源的需求，尤其是显式溶剂模型，在很大程度上限制了其应用。在本研究中，以腺苷酸激酶为例评估了速度缩放 REMD (vsREMD) 变体的可用性和效率。尽管 vsREMD 取得了与传统 REMD 和实验研究一致的结果，但 vsREMD (30) 所需的副本数量远少于传统 REMD (80) 以达到相似的接受率 (~0.2)，证明了高效率vsREMD 来表征蛋白质构象变化和相关的自由能曲线。因此，