Find slow dynamic modes via analyzing molecular dynamics simulation trajectories  

作　　者：Chuanbiao Zhang Xin Zhou 张传彪;周昕(College of Physics and Electronic Engineering,Heze University,Heze 274015,China;School of Physical Sciences,University of Chinese Academy of Sciences,Beijing 100190,China)

机构地区：[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

出　　处：《Chinese Physics B》2020年第10期33-39,共7页中国物理B（英文版）

基　　金：Project supported by the National Natural Science Foundation of China (Grant No. 11904086).

摘　　要：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.

关 键 词：molecular dynamics simulation slow modes trajectory map 

分 类 号：Q617[生物学—生物物理学]