Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices.

ABSTRACT: Most chemical transformations (reactions or conformational changes) that are of interest to researchers have many degrees of freedom, usually too many to visualize without reducing the dimensionality of the system to include only the most important atomic motions. In this article, we describe a method of using Principal Component Analysis (PCA) for analyzing a series of molecular geometries (e.g., a reaction pathway or molecular dynamics trajectory) and determining the reduced dimensional space that captures the most structural variance in the fewest dimensions. The software written to carry out this method is called PathReducer, which permits (1) visualizing the geometries in a reduced dimensional space, (2) determining the axes that make up the reduced dimensional space, and (3) projecti

SUBMITTER: Hare SR 

PROVIDER: S-EPMC6991188 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature