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A sampling problem in molecular dynamics simulations of macromolecules.
Open accessAbstract
Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.
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Cited by
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Making optimal use of empirical energy functions: Force‐field parameterization in crystal space
Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A., & Vriend, G. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20251 · Cited by 853
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Metadata
- Authors
- Clarage, J. B., Romo, T., Andrews, B. K., Pettitt, B. M., & Phillips, G. N.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1995-04-11
- Volume
- 92
- Issue
- 8
- Pages
- 3288-3292
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2010200494
- Cited by
- 196
- References
- 0
- FWCI
- 5.09
- Type
- journal article
- Language
- en
- Open access
- green
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- Clarage, J. B., Romo, T., Andrews, B. K., Pettitt, B. M., & Phillips, G. N. (1995). A sampling problem in molecular dynamics simulations of macromolecules. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.92.8.3288
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