Galvelis Raimondas, Sugita Yuji
RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
RIKEN Advance Institute for Computational Science, 7-1-26 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
J Comput Chem. 2015 Jul 15;36(19):1446-55. doi: 10.1002/jcc.23945. Epub 2015 May 19.
Metadynamics (MTD) is a powerful enhanced sampling method for systems with rugged energy landscapes. It constructs a bias potential in a predefined collective variable (CV) space to overcome barriers between metastable states. In bias-exchange MTD (BE-MTD), multiple replicas approximate the CV space by exchanging bias potentials (replica conditions) with the Metropolis-Hastings (MH) algorithm. We demonstrate that the replica-exchange rates and the convergence of free energy estimates of BE-MTD are improved by introducing the infinite swapping (IS) or the Suwa-Todo (ST) algorithms. Conceptually, IS and ST perform transitions in a replica state space rather than exchanges in a replica condition space. To emphasize this, the proposed scheme is called the replica state exchange MTD (RSE-MTD). Benchmarks were performed with alanine polypeptides in vacuum and water. For the systems tested in this work, there is no significant performance difference between IS and ST.
元动力学（MTD）是一种用于具有崎岖能量景观系统的强大增强采样方法。它在预定义的集体变量（CV）空间中构建一个偏差势，以克服亚稳态之间的势垒。在偏差交换MTD（BE-MTD）中，多个副本通过使用Metropolis-Hastings（MH）算法交换偏差势（副本条件）来近似CV空间。我们证明，通过引入无限交换（IS）或Suwa-Todo（ST）算法，可以提高BE-MTD的副本交换率和自由能估计的收敛性。从概念上讲，IS和ST在副本状态空间中执行转换，而不是在副本条件空间中进行交换。为强调这一点，所提出的方案称为副本状态交换MTD（RSE-MTD）。在真空和水中对丙氨酸多肽进行了基准测试。对于本工作中测试的系统，IS和ST之间没有显著的性能差异。
