The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
Harmonic analysis of large systems. I. Methodology
Abstract
Methods have been developed for the determination of vibrational frequencies and normal modes of large systems in the full conformational space (including all degrees of freedom) and in a reduced conformational space (reducing the number of degrees of freedom). The computational method, which includes Hessian generation and storage, full and iterative diagonalization techniques, and the refinement of the results, is presented. A method is given for the quasiharmonic analysis and the reduced basis quasiharmonic analysis. The underlying principle is that from the atomic fluctuations, an effective harmonic force field can be determined relative to the dynamic average structure. Normal mode analysis tools can be used to characterize quasiharmonic modes of vibration. These correspond to conventional normal modes except that anharmonic effects are included. Numerous techniques for the analyses of vibrational frequencies and normal modes are described. Criteria for the analysis of the similarity of low‐frequency normal modes is presented. The approach to determining the natural frequencies and normal modes of vibration described here is general and applicable to any large system. © 1995 John Wiley & Sons, Inc.This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
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Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 21,239
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 14,944
Self-citationLanczos, C. (1950) · Journal of Research of the National Bureau of Standards · doi:10.6028/jres.045.026 · Cited by 4,391
Algorithms for macromolecular dynamics and constraint dynamics
van Gunsteren, W. F., & Berendsen, H. J. C. (1977) · Molecular Physics · doi:10.1080/00268977700102571 · Cited by 1,732
Method for estimating the configurational entropy of macromolecules
Karplus, M., & Kushick, J. N. (1981) · Macromolecules · doi:10.1021/ma50003a019 · Cited by 849
Self-citationHarmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.
Brooks, B., & Karplus, M. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.21.6571 · Cited by 829
Self-citationDynamics of a small globular protein in terms of low-frequency vibrational modes.
Go, N., Noguti, T., & Nishikawa, T. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.12.3696 · Cited by 722
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
Levitt, M., Sander, C., & Stern, P. S. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90230-x · Cited by 721
(1975) · Royal Society of Chemistry eBooks · doi:10.1039/9781847556936 · Cited by 705
DYNAMICS OF PROTEINS: ELEMENTS AND FUNCTION
Kurplus, M., & McCammon, J. A. (1983) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.52.070183.001403 · Cited by 685
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Metadata
- Authors
- Brooks, B. R., Janežič, D., & Karplus, M.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 1995-12
- Volume
- 16
- Issue
- 12
- Pages
- 1522-1542
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2093151204
- Cited by
- 489
- References
- 22
- FWCI
- 2.96
- Type
- journal article
- Language
- en
- Open access
- closed
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