Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell Jr., Klaus
Schulten, and Benoît Roux.
High-performance scalable molecular dynamics simulations of a
polarizable force field based on classical Drude oscillators in NAMD.
Journal of Physical Chemistry Letters, 2:87-92, 2011.
JIAN2011
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 fidelity. 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 based on this model in the MD simulation
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. To validate and evaluate the
performance of NAMD, structural and transport properties were characterized for a series
of systems.
Excellent agreement with experiments and previous simulations are obtained. It is shown
that large-scale MD simulations based on the Drude polarizable force field scale very well
on massively distributed supercomputing platforms. The cost of simulations based on the
Drude model is only - higher than those based on nonpolarizable
models.
-
higher than those based on nonpolarizable
models.
