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

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

SUBMITTER: Jiang W 

PROVIDER: S-EPMC3092300 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature