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

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TitleHigh-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.
Publication TypeJournal Article
Year of Publication2011
AuthorsJiang, W, Hardy, DJ, Phillips, JC, Mackerell, AD, Schulten, K, Roux, B
JournalJ Phys Chem Lett
Volume2
Issue2
Pagination87-92
Date Published2011
ISSN1948-7185
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.

DOI10.1021/jz101461d
Alternate JournalJ Phys Chem Lett
PubMed ID21572567
PubMed Central IDPMC3092300
Grant ListR01 GM072558 / GM / NIGMS NIH HHS / United States
R01 GM070855 / GM / NIGMS NIH HHS / United States
P41 RR005969 / RR / NCRR NIH HHS / United States
R01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States
R01 GM072558-08 / GM / NIGMS NIH HHS / United States