Journal of Molecular Modeling

, 24:221 | Cite as

Indices to evaluate the reliability of coarse-grained representations of mixed inter/intramolecular vibrations

  • Makoto Isogai
  • Hirohiko Houjou
Original Paper


We propose some methods for quantifying the reliability of coarse-grained representations of displacement vectors of normal mode vibrations. In the framework of our basic theory, the original displacement vectors are projected onto a lower-dimensional (i.e., a coarse-grained) space. Four types of functions denoted fidelity indices were introduced as measures of the similarity of the original to the restored displacement vectors. These indices were applied to several hydrogen-bonded homodimers, and the behavior of each index was examined. We found that a coarse-grained representation with high reliability resulted in the accurate restoration of properties such as eigenfrequency, modal mass, and modal stiffness.


Molecular vibration Coarse graining Molecular assembly Normal mode analysis GF matrix method 



This work was supported (in part) by a Grant for Basic Science Research Project in the fiscal year of 2016 received from The Sumitomo Foundation.


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute of Industrial ScienceThe University of TokyoTokyoJapan

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