Czaplewski Cezary, Kalinowski Sebastian, Liwo Adam, Scheraga Harold A
Baker Laboratory of Chemisty and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and, Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.
J Chem Theory Comput. 2009 Mar 10;5(3):627-640. doi: 10.1021/ct800397z.
The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster.
副本交换（RE）方法在生物分子系统的分子动力学（MD）模拟中越来越多地用于改善采样。最近，我们为介观MD实现了联合残基UNRES力场。UNRES MD模拟的初步结果表明，我们能够模拟在微秒甚至毫秒时间尺度上发生的折叠事件。为了进一步加快搜索速度，我们应用了多路复用副本交换分子动力学（MREMD）方法。由Rhee和Pande开发的RE方法的多路复用变体（MREMD）与原始RE方法的不同之处在于，在给定温度下运行多条轨迹。在不同温度下运行的每组轨迹构成一层。不仅在单层内而且在层间都尝试进行交换。该代码已并行化，可扩展至4000个处理器。我们展示了使用UNRES力场对蛋白质折叠进行正则MD、REMD和MREMD模拟的比较。我们证明，多路复用过程大大提高了副本交换MD的能力，并且热力学量的收敛速度更快。
