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

Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell, Klaus Schulten, Benoît Roux

Research output: Contribution to journalArticlepeer-review

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 increasing by only a factor of 1.2 to 1.8 compared to 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.

Original languageEnglish (US)
Pages (from-to)87-92
Number of pages6
JournalJournal of Physical Chemistry Letters
Volume2
Issue number2
DOIs
StatePublished - Jan 20 2011

Keywords

  • General Theory
  • Molecular Structure
  • Quantum Chemistry

ASJC Scopus subject areas

  • Materials Science(all)

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