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.
%0 Journal Article
%1 doi:10.1021/ct400403y
%A Rühle, Victor
%A Kusumaatmaja, Halim
%A Chakrabarti, Dwaipayan
%A Wales, David J.
%D 2013
%J Journal of Chemical Theory and Computation
%K classical coordinate mechanics physics transform unread
%N 9
%P 4026-4034
%R 10.1021/ct400403y
%T Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules
%U http://pubs.acs.org/doi/abs/10.1021/ct400403y
%V 9
%X 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.
@article{doi:10.1021/ct400403y,
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. },
added-at = {2013-09-24T15:14:06.000+0200},
author = {Rühle, Victor and Kusumaatmaja, Halim and Chakrabarti, Dwaipayan and Wales, David J.},
biburl = {https://www.bibsonomy.org/bibtex/240d9ede26f0dc7aed3fda606705171a3/drmatusek},
doi = {10.1021/ct400403y},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/ct400403y},
interhash = {e2d90c1f2ee18c605bc2af6ed0613d25},
intrahash = {40d9ede26f0dc7aed3fda606705171a3},
journal = {Journal of Chemical Theory and Computation},
keywords = {classical coordinate mechanics physics transform unread},
month = sep,
number = 9,
pages = {4026-4034},
timestamp = {2013-09-24T15:14:06.000+0200},
title = {Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules},
url = {http://pubs.acs.org/doi/abs/10.1021/ct400403y},
volume = 9,
year = 2013
}