Paper Citing NAMD - Abstract
Jiang, Wei; Hardy, David J.; Phillips, James C.; MacKerell, Alexander D., Jr.; Schulten, Klaus; Roux, Benoit
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, JAN 20 2011
Incorporating the influence of induced polarization in large-scale atmositic molecular dynamics (MD) simulations is a critical challenge in the progress toward computations of increased accuracy. One compuationally 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.
