Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi, 444-8585, Japan.
J Comput Chem. 2013 Nov 5;34(29):2493-7. doi: 10.1002/jcc.23402. Epub 2013 Aug 7.
We propose the Hamiltonian replica-permutation method (RPM) (or multidimensional RPM) for molecular dynamics and Monte Carlo simulations, in which parameters in the Hamiltonian are permuted among more than two replicas with the Suwa-Todo algorithm. We apply the Coulomb RPM, which is one of realization of the Hamiltonian RPM, to an alanine dipeptide and to two amyloid-β(29-42) molecules. The Hamiltonian RPM realizes more efficient sampling than the Hamiltonian replica-exchange method. We illustrate the protein misfolding funnel of amyloid-β(29-42) and reveal its dimerization pathways.
我们提出了用于分子动力学和蒙特卡罗模拟的哈密顿复制-置换方法（RPM）（或多维 RPM），其中哈密顿量中的参数通过 Suwa-Todo 算法在两个以上的副本之间进行置换。我们将库仑 RPM（哈密顿 RPM 的一种实现）应用于丙氨酸二肽和两个淀粉样β（29-42）分子。哈密顿 RPM 比哈密顿复制交换方法实现了更有效的采样。我们说明了淀粉样β（29-42）的蛋白质错误折叠漏斗，并揭示了其二聚化途径。
