Find slow dynamic modes via analyzing molecular dynamics simulation trajectories

doi:10.1088/1674-1056/abad24

中国物理B ›› 2020, Vol. 29 ›› Issue (10): 108706-.doi: 10.1088/1674-1056/abad24

所属专题： SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids

Chuanbiao Zhang(张传彪)¹, Xin Zhou(周昕)²^,†()

收稿日期:2020-06-18 修回日期:2020-07-27 接受日期:2020-08-07 出版日期:2020-10-05 发布日期:2020-10-05
通讯作者: Xin Zhou(周昕)

Find slow dynamic modes via analyzing molecular dynamics simulation trajectories

Chuanbiao Zhang(张传彪)¹ and Xin Zhou(周昕)^2,†

¹ College of Physics and Electronic Engineering, Heze University, Heze 274015, China
² School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China

Received:2020-06-18 Revised:2020-07-27 Accepted:2020-08-07 Online:2020-10-05 Published:2020-10-05
Contact: ^†Corresponding author. E-mail: xzhou@ucas.ac.cn
About author:
†Corresponding author. E-mail: xzhou@ucas.ac.cn
* Project supported by the National Natural Science Foundation of China (Grant No. 11904086).

摘要/Abstract

Abstract:

It is a central issue to find the slow dynamic modes of biological macromolecules via analyzing the large-scale data of molecular dynamics simulation (MD). While the MD data are high-dimensional time-successive series involving all-atomic details and sub-picosecond time resolution, a few collective variables which characterizing the motions in longer than nanoseconds are needed to be chosen for an intuitive understanding of the dynamics of the system. The trajectory map (TM) was presented in our previous works to provide an efficient method to find the low-dimensional slow dynamic collective-motion modes from high-dimensional time series. In this paper, we present a more straight understanding about the principle of TM via the slow-mode linear space of the conformational probability distribution functions of MD trajectories and more clearly discuss the relation between the TM and the current other similar methods in finding slow modes.

Key words: molecular dynamics simulation, slow modes, trajectory map

中图分类号: (Theory, modeling, and computer simulation)

87.15.A-

02.70.Ns (Molecular dynamics and particle methods) 82.20.Wt (Computational modeling; simulation)

Chuanbiao Zhang(张传彪), Xin Zhou(周昕). [J]. 中国物理B, 2020, 29(10): 108706-.

Chuanbiao Zhang(张传彪) and Xin Zhou(周昕)†. Find slow dynamic modes via analyzing molecular dynamics simulation trajectories[J]. Chin. Phys. B, 2020, 29(10): 108706-.

图/表 2

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Find slow dynamic modes via analyzing molecular dynamics simulation trajectories

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