Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices

08 May 2019, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Low dimensional representations along reaction pathways were produced using newly created Python software that utilises Principal Component Analysis (PCA) to do dimensionality reduction. Plots of these pathways in reduced dimensional space, as well as the physical meaning of the reduced dimensional axes, are discussed.

Keywords

Dimensionality reduction
PCA
Reaction Coordinates
Molecular Dynamics

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