Reweighted ensemble dynamics simulations: Theory, improvement, and application

doi:10.1088/1674-1056/24/6/060202

Abstract

Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provide schemes on selection of basis functions, and determination of the free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enables us to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in an entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.

Keywords: ensemble dynamics simulations peptides enhanced sampling metastable states

Received: 20 November 2014
Revised: 19 January 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

About author: 02.70.Ns; 87.15.A-; 82.20.Wt

Cite this article:

Gong Lin-Chen (龚麟宸), Zhou Xin (周昕), Ouyang Zhong-Can (欧阳钟灿) Reweighted ensemble dynamics simulations: Theory, improvement, and application 2015 Chin. Phys. B 24 060202

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