DOI: 10.1073/pnas.92.8.3288. A sampling problem in molecular dynamics simulations of macromolecules.

A sampling problem in molecular dynamics simulations of macromolecules.

10.1073/pnas.92.8.3288

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

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.

Bibliography

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, 92(8), 3288â3292.

Authors 5

J B Clarage (first)
T Romo (additional)
B K Andrews (additional)
B M Pettitt (additional)
G N Phillips (additional)

References 0 Referenced 184

None

Dates

Type	When
Created	19 years, 2 months ago (May 31, 2006, 9:31 a.m.)
Deposited	3 years, 4 months ago (April 13, 2022, 2:06 p.m.)
Indexed	1 month ago (July 28, 2025, 2:38 a.m.)
Issued	30 years, 4 months ago (April 11, 1995)
Published	30 years, 4 months ago (April 11, 1995)
Published Online	30 years, 4 months ago (April 11, 1995)
Published Print	30 years, 4 months ago (April 11, 1995)

Funders 0

None

BibTeX

@article{Clarage_1995, title={A sampling problem in molecular dynamics simulations of macromolecules.}, volume={92}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.92.8.3288}, DOI={10.1073/pnas.92.8.3288}, number={8}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Clarage, J B and Romo, T and Andrews, B K and Pettitt, B M and Phillips, G N}, year={1995}, month=apr, pages={3288–3292} }

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