The construction of general basis functions in reweighting ensemble dynamics simulations: Reproduce equilibrium distribution in complex systems from multiple short simulation trajectories

doi:10.1088/1674-1056/24/12/120202

Abstract Ensemble simulations, which use multiple short independent trajectories from dispersive initial conformations, rather than a single long trajectory as used in traditional simulations, are expected to sample complex systems such as biomolecules much more efficiently. The re-weighted ensemble dynamics (RED) is designed to combine these short trajectories to reconstruct the global equilibrium distribution. In the RED, a number of conformational functions, named as basis functions, are applied to relate these trajectories to each other, then a detailed-balance-based linear equation is built, whose solution provides the weights of these trajectories in equilibrium distribution. Thus, the sufficient and efficient selection of basis functions is critical to the practical application of RED. Here, we review and present a few possible ways to generally construct basis functions for applying the RED in complex molecular systems. Especially, for systems with less priori knowledge, we could generally use the root mean squared deviation (RMSD) among conformations to split the whole conformational space into a set of cells, then use the RMSD-based-cell functions as basis functions. We demonstrate the application of the RED in typical systems, including a two-dimensional toy model, the lattice Potts model, and a short peptide system. The results indicate that the RED with the constructions of basis functions not only more efficiently sample the complex systems, but also provide a general way to understand the metastable structure of conformational space.

Keywords: ensemble simulation equilibrium distribution reweighting basis functions peptide

Received: 12 June 2015
Revised: 14 September 2015
Accepted manuscript online:

PACS:	02.70.Ns	(Molecular dynamics and particle methods)
	87.15.A-	(Theory, modeling, and computer simulation)
	82.20.Wt	(Computational modeling; simulation)

Fund: Project supported by the National Natural Science Foundation of China (Grant No. 11175250).

Corresponding Authors: Zhou Xin
E-mail: xzhou@ucas.ac.cn

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Zhang Chuan-Biao (张传彪), Li Ming (黎明), Zhou Xin (周昕) The construction of general basis functions in reweighting ensemble dynamics simulations: Reproduce equilibrium distribution in complex systems from multiple short simulation trajectories 2015 Chin. Phys. B 24 120202

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The construction of general basis functions in reweighting ensemble dynamics simulations: Reproduce equilibrium distribution in complex systems from multiple short simulation trajectories

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