Physics – Condensed Matter – Statistical Mechanics
Scientific paper
2009-11-18
Physics
Condensed Matter
Statistical Mechanics
24 pages, 8 figures
Scientific paper
Based on multiple short simulation trajectories started from dispersively selected initial conformations, the weighted ensemble dynamics (WED) method [Phys Rev. E,80, 026707 (2009)] has been designed to explore the hierarchical state structure in conformational space. In this article, we have further improved the WED method. Several schemes have been designed respectively for reducing the statistical error, systematically selecting the physical variables in analysis and determining the only adjustable parameter of WED. Besides, we illustrate the application of WED in more complicated examples, including a system with transition network between multiple states, a system with entropy-dominated state, and the low-temperature simulation of solvated alanine dipeptide. WED is found to correctly capture the topology of the transition networks of the model systems. It can also identify the solvent effect for the solvated alanine dipeptide system, as well as the diffusion-like dynamical behavior both for the entropy-dominated system and the low-temperature simulation of solvated alanine dipeptide. These examples will serve as the references for the application of WED to more complicated biological macromolecules.
Gong Linchen
Zhou Xin
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