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The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
Abstract
Simulations of the HIV-1 protease unit cell using a 9 Å cutoff, 9/18 Å ‘‘twin-range’’ cutoff, and full Ewald sums have been carried out to 300 ps. The results indicate that long-range electrostatic interactions are essential for proper representation of the HIV-1 protease crystal structure. The 9 Å simulation did not converge in 300 ps. Inclusion of a 9/18 Å ‘‘twin-range’’ cutoff showed significant improvement. Simulation using the Ewald summation convention gave the best overall agreement with x-ray crystallographic data, and showed the least internal differences in the time average structures of the asymmetric units. The Ewald simulation represents an efficient implementation of the Particle Mesh Ewald method [Darden et al., J. Chem. Phys. 98, 10 089 (1993)], and illustrates the importance of including long-range electrostatic forces in large macromolecular systems.
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Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
Cited by
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Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470117 · Cited by 22,514
Self-citationShea, J.-E., & Brooks III, C. L. (2001) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.52.1.499 · Cited by 481
Adsorption behaviors of shale oil in kerogen slit by molecular simulation
Yang, Y., Liu, J., Yao, J., Kou, J., Li, Z., Wu, T., Zhang, K., Zhang, L., & Sun, H. (2020) · Chemical Engineering Journal · doi:10.1016/j.cej.2020.124054 · Cited by 298
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Metadata
- Authors
- York, D. M., Darden, T. A., & Pedersen, L. G.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 1993-11-15
- Volume
- 99
- Issue
- 10
- Pages
- 8345-8348
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2025768791
- Cited by
- 755
- References
- 1
- FWCI
- 1.87
- Type
- journal article
- Language
- en
- Open access
- closed
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- York, D. M., Darden, T. A., & Pedersen, L. G. (1993). The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods. The Journal of Chemical Physics. https://doi.org/10.1063/1.465608
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
