Exploring energy landscapes: metrics, pathways, and normal mode analysis for rigid-body molecules

Rühle, V.; Kusumaatmaja, H.; Chakrabarti, D.; Wales, D.J.

Abstract

We present new methodology for exploring the energy landscapes of molecular systems, using angle-axis variables for the rigid-body rotational coordinates. The key ingredient is a distance measure or metric tensor, which is invariant to global translation and rotation. The metric is used to formulate a generalized nudged elastic band method for calculating pathways, and a full prescription for normal-mode analysis is described. The methodology is tested by mapping the potential energy and free energy landscape of the water octamer, described by the TIP4P potential.

Citation

Rühle, V., Kusumaatmaja, H., Chakrabarti, D., & Wales, D. (2013). Exploring energy landscapes: metrics, pathways, and normal mode analysis for rigid-body molecules. Journal of Chemical Theory and Computation, 9(9), 4026-4034. https://doi.org/10.1021/ct400403y

• Journal Article Type: Article
• Publication Date: Sep 10, 2013
• Deposit Date: Aug 29, 2014
• Publicly Available Date: Sep 3, 2014
• Journal: Journal of Chemical Theory and Computation
• Print ISSN: 1549-9618
• Electronic ISSN: 1549-9626
• Publisher: American Chemical Society
• Peer Reviewed: Peer Reviewed
• Volume: 9
• Issue: 9
• Pages: 4026-4034
• DOI: https://doi.org/10.1021/ct400403y
• Public URL: https://durham-repository.worktribe.com/output/1446137