TCB Publications - Abstract

TCB Publications - Abstract

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. (PMC: 3092300)

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.

Download Full Text

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper's publisher and author. You may not upload any of this site's material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this web site is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

Download full text: Journal, Request a Copy