A case study of truncated electrostatics for simulation of polyelectrolyte brushes on GPU accelerators

Trung Dac Nguyen, Jan Michael Y. Carrillo, Andrey V. Dobrynin, W. Michael Brown*

*Corresponding author for this work

Research output: Contribution to journalArticle

15 Scopus citations

Abstract

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 (P3M) method for the molecular dynamics simulation of polyelectrolyte brush layers. We show that with the use of GPU accelerators, large parallel simulations using P3M 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 P 3M 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 P3M; for these systems, computationally efficient parametrizations of the truncation-based approach do not produce accurate counterion density profiles or brush morphologies.

Original languageEnglish (US)
Pages (from-to)73-83
Number of pages11
JournalJournal of Chemical Theory and Computation
Volume9
Issue number1
DOIs
StatePublished - Jan 8 2013

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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