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Ozog, D., Malony, A. D., & Guenza, M. (2016, February). The UA? CG Workflow: High Performance Molecular Dynamics of Coarse-Grained Polymers. In Parallel, Distributed, and Network-Based Processing (PDP), 2016 24th Euromicro International Conference on (pp. 272-279). IEEE.

Keywords: -atomistic simulation, coarse-graining, scientific workflows, polymeric liquids, LAMMPS

—Our analytically based technique for coarsegraining (CG) polymer simulations dramatically improves spatial and temporal scaling while preserving thermodynamic quantities and bulk properties. The purpose of CG codes is to run more efficient molecular dynamics simulations, yet the research field generally lacks thorough analysis of how such codes scale with respect to full-atom representations. This paper conducts an in-depth performance study of highly realistic polymer melts on modern supercomputing systems. We also present a workflow that integrates our analytical solution for calculating CG forces with new high-performance techniques for mapping back and forth between the atomistic and CG descriptions in LAMMPS. The workflow benefits from the performance of CG, while maintaining full-atom accuracy. Our results show speedups up to 12x faster than atomistic simulations.


Created: Fri Jan 20 14:40:23 2017

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