TCB Publications - Paper Request

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 $50\%$-$100\%$ higher than those based on nonpolarizable models.

Request Paper

Full Name
Email Address
Type the number seven in the box