Metrics for measuring distances in configuration spaces

Journal of Chemical Physics - Tập 139 Số 18 - 2013
Ali Sadeghi1, S. Alireza Ghasemi1, Bastian Schaefer1, Stephan Mohr1, Markus A. Lill2, Stefan Goedecker1
1Universität Basel 1 Department of Physics, , Klingelbergstr. 82, 4056 Basel, Switzerland
2Purdue University 2 Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, , 575 Stadium Mall Drive, West Lafayette, Indiana 47907, USA

Tóm tắt

In order to characterize molecular structures we introduce configurational fingerprint vectors which are counterparts of quantities used experimentally to identify structures. The Euclidean distance between the configurational fingerprint vectors satisfies the properties of a metric and can therefore safely be used to measure dissimilarities between configurations in the high dimensional configuration space. In particular we show that these metrics are a perfect and computationally cheap replacement for the root-mean-square distance (RMSD) when one has to decide whether two noise contaminated configurations are identical or not. We introduce a Monte Carlo approach to obtain the global minimum of the RMSD between configurations, which is obtained from a global minimization over all translations, rotations, and permutations of atomic indices.

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Journal of Chemical Physics

Tập 139 Số 18

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