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P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
Abstract
By removing the fastest degrees of freedom, constraints allow for an increase of the time step in molecular simulations. In the last decade parallel simulations have become commonplace. However, up till now efficient parallel constraint algorithms have not been used with domain decomposition. In this paper the parallel linear constraint solver (P-LINCS) is presented, which allows the constraining of all bonds in macromolecules. Additionally the energy conservation properties of (P-)LINCS are assessed in view of improvements in the accuracy of uncoupled angle constraints and integration in single precision.
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Cited by
Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015) · SoftwareX · doi:10.1016/j.softx.2015.06.001 · Cited by 27,190
Self-citationComputer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor
Yang, J., Petitjean, S. J. L., Koehler, M., Zhang, Q., Dumitru, A. C., Chen, W., Derclaye, S., Vincent, S. P., Soumillion, P., & Alsteens, D. (2020) · Nature Communications · doi:10.1038/s41467-020-18319-6 · Cited by 615
Molecular origins of fluorocarbon hydrophobicity
Dalvi, V. H., & Rossky, P. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0915169107 · Cited by 421
Accurate calculation of the absolute free energy of binding for drug molecules
Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., & Biggin, P. C. (2016) · Chemical Science · doi:10.1039/c5sc02678d · Cited by 347
Metadata
- Authors
- Hess, B.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-12-01
- Volume
- 4
- Issue
- 1
- Pages
- 116-122
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2059013803
- Cited by
- 3,987
- References
- 0
- FWCI
- 12.35
- Type
- journal article
- Language
- en
- Open access
- closed
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