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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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Self-citation
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Lemkul, J. A., Huang, J., Roux, B., & MacKerell, A. D. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00505 · Cited by 623
Self-citationPolarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
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Self-citationCHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., et al. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c04100 · Cited by 136
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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