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Abstract
摘要 |
It is a difficult task to detect equilibrium and dynamical properties in complex molecular systems due to the existence of high entropic-dominated free-energy barriers. The kinetic network included metastable conformational regions and transitions among the regions in different time scales provides a possible way to understand the complex systems. Based on multiple molecular-dynamic simulation trajectories started from dispersively selected initial conformations, weighted ensemble dynamics (WED) method is designed to robustly and systematically explore the hierarchical metastable structure, through the spectral analysis of the variance-covariance matrix of trajectory-mapped vectors. Non-degenerate ground state of the matrix directly predicts the ergodicity of simulation data. The ground state could be adopted as statistical weights of trajectories to correctly reconstruct global equilibrium properties, even though each trajectory only explores part of the conformational space. Otherwise, the degree of degeneracy simply gives the number of metastable states of the system under the time scale of individual trajectory. Manipulation on the eigenvectors leads to the classification of trajectories into non-transition ones within the states and transition ones between them. The transition states and kinetics are also predicted without priori knowledge of the system. We demonstrate the application of the general method to some systems, invoves polypeptide with explicit and implicit solvent. |
