alexa High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.
Biomedical Sciences

Biomedical Sciences

Journal of Bioanalysis & Biomedicine

Author(s): Jiang W, Hardy DJ, Phillips JC, Mackerell AD Jr, Schulten K,

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Abstract 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.
This article was published in J Phys Chem Lett and referenced in Journal of Bioanalysis & Biomedicine

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