Laboratory for Computational Molecular Design, RIKEN QBiC (Quantitative Biology Center), 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
J Chem Phys. 2013 Jun 28;138(24):244113. doi: 10.1063/1.4811711.
The replica exchange method (REM) is a powerful tool for the conformational sampling of biomolecules. In this study, we propose an enhanced exchange algorithm for REM not meeting the detailed balance condition (DBC), but satisfying the balance condition in all considered exchanges between two replicas. Breaking the DBC can minimize the rejection rate and make an exchange process rejection-free as the number of replicas increases. To enhance the efficiency of REM, all possible pairs--not only the nearest neighbor--were considered in the exchange process. The test simulations of the alanine dipeptide confirmed the correctness of our method. The average traveling distance of each replica in the temperature distribution was also increased in proportion to an increase in the exchange rate. Furthermore, we applied our algorithm to the conformational sampling of the 10-residue miniprotein, chignolin, with an implicit solvent model. The results showed a faster convergence in the calculation of its free energy landscape, compared to that achieved using the normal exchange method of adjacent pairs. This algorithm can also be applied to the conventional near neighbor method and is expected to reduce the required number of replicas.
置换交换方法 (REM) 是一种对生物分子构象进行采样的强大工具。在这项研究中，我们提出了一种增强的置换交换算法，该算法不满足详细平衡条件 (DBC)，但满足两个副本之间所有考虑的交换中的平衡条件。打破 DBC 可以最小化拒绝率，并使交换过程在增加副本数量时无拒绝。为了提高 REM 的效率，在交换过程中考虑了所有可能的对——不仅是最近邻。丙氨酸二肽的测试模拟证实了我们方法的正确性。每个副本在温度分布中的平均行程距离也随着交换率的增加而成比例增加。此外，我们将我们的算法应用于 10 残基小蛋白 chignolin 的构象采样，采用隐溶剂模型。与使用相邻对的常规交换方法相比，该算法在计算其自由能景观时表现出更快的收敛速度。该算法还可以应用于传统的近邻方法，并有望减少所需的副本数量。
