The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD
Open accessAbstract
Incorporating the influence of induced polarization in large-scale atomistic molecular dynamics (MD) simulations is a critical challenge in the progress toward computations of increased accuracy. One computationally efficient treatment is based on the classical Drude oscillator in which an auxiliary charged particle is attached by a spring to each nucleus. Here, we report the first implementation of this model in the program NAMD. An extended Lagrangian dynamics with a dual-Langevin thermostat scheme applied to the Drude-nucleus pairs is employed to efficiently generate classical dynamic propagation near the self-consistent field limit. Large-scale MD simulations based on the Drude polarizable force field scale very well on massively distributed supercomputing platforms, the computational demand being only about 50-100% higher than for nonpolarizable models. As an illustration, a large-scale 150 mM NaCl aqueous salt solution is simulated, and the calculated ionic conductivity is shown to be in excellent agreement with experiment.
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Cites
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Scalable molecular dynamics on CPU and GPU architectures with NAMD
Phillips, J. C., Hardy, D. J., Maia, J. D. C., Stone, J. E., Ribeiro, J. V., Bernardi, R. C., Buch, R., Fiorin, G., Hénin, J., Jiang, W., et al. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0014475 · Cited by 3,144
Self-citationBiomolecular Simulation: A Computational Microscope for Molecular Biology
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Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields
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Self-citationPolarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
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Self-citation
Metadata
- Authors
- Jiang, W., Hardy, D. J., Phillips, J. C., MacKerell, A. D., Schulten, K., & Roux, B.
- Venue
- The Journal of Physical Chemistry Letters
- Publisher
- American Chemical Society (ACS)
- Published
- 2010-12-23
- Volume
- 2
- Issue
- 2
- Pages
- 87-92
- ISSN
- 1948-7185 (ISSN-L)
- OpenAlex
- W1972399880
- Cited by
- 279
- References
- 30
- FWCI
- 7.58
- Type
- journal article
- Language
- en
- Open access
- green
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