A Case Study of Truncated Electrostatics for Simulation of Polyelectrolyte Brushes on GPU Accelerators

TD Nguyen and JMY Carrillo and AV Dobrynin and WM Brown, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9, 73-83 (2013).

DOI: 10.1021/ct300718x

Numerous issues have disrupted the trend for increasing computational performance with faster CPU clock frequencies. In order to exploit the potential performance of new computers, it is becoming increasingly desirable to re-evaluate computational physics methods and models with an eye toward approaches that allow for increased concurrency and data locality. The evaluation of long-range Coulombic interactions is a common bottleneck for molecular dynamics simulations. Enhanced truncation approaches have been proposed as an alternative method and are particularly well-suited for many-core architectures and GPUs due to the inherent fine-grain parallelism that can be exploited. In this paper, we compare efficient truncation-based approximations to evaluation of electrostatic forces with the more traditional particle particle-particle-mesh ((PM)-M-3) method for the molecular dynamics simulation of polyelectrolyte brush layers. We show that with the use of GPU accelerators, large parallel simulations using (PM)-M-3 can be greater than 3 times faster due to a reduction in the mesh-size required. Alternatively, using a truncation-based scheme can improve performance even further. This approach can be up to 3.9 times faster than GPU-accelerated (PM)-M-3 for many polymer systems and results in accurate calculation of shear velocities and disjoining pressures for brush layers. For configurations with highly nonuniform charge distributions, however, we find that it is more efficient to use (PM)-M-3; for these systems, computationally efficient parametrizations of the truncation-based approach do not produce accurate counterion density profiles or brush morphologies.

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