Investigation of Cooperative Modes for Collective Molecules Using Grid-Based Principal Component Analysis

• Published in: The journal of physical chemistry. B Vol. 125; no. 4; pp. 1072 - 1084
• Main Author: Ogata, Koji
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 04.02.2021
• Subjects: B: Biophysical and Biochemical Systems and Processes; liquids; methane; molecular dynamics; Molecular Dynamics Simulation; Motion; Principal Component Analysis; Protein Conformation; protein domains; Proteins

A grid-based principal component analysis method (GBPCA) has been developed and implemented to investigate the modes of collective molecules present in the cube in the grid system from their trajectories using molecular dynamics (MD) simulation. This method is applied to the simulations of water, me...