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Parallel Adaptively Restrained Molecular Dynamics

Krishna Singh 1 Dmitriy Marin 1 Stephane Redon 1
1 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, Grenoble INP - Institut polytechnique de Grenoble - Grenoble Institute of Technology, LJK - Laboratoire Jean Kuntzmann
Abstract : Force computations are one of the most time consuming part in performing Molecular Dynamics (MD) simulations. Adaptively Restrained Molecular Dynamics (ARMD) makes it possible to perform fewer force calculations by adap-tively restraining particles positions. This paper introduces parallel algorithms for single-pass incremental force computations to take advantage of adaptive restraints using the Message Passage Interface (MPI) standard. The proposed algorithms are implemented and validated in LAMMPS, however, these algorithms can be applied to other MD simulators. We compared our algorithms with LAMMPS for performance and scalability measurements.
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https://hal.inria.fr/hal-01591466
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Submitted on : Friday, September 22, 2017 - 10:51:30 AM
Last modification on : Tuesday, November 24, 2020 - 5:04:04 PM
Long-term archiving on: : Saturday, December 23, 2017 - 12:18:06 PM

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Krishna Singh, Dmitriy Marin, Stephane Redon. Parallel Adaptively Restrained Molecular Dynamics. 2017 International Conference on High Performance Computing & Simulation (HPCS), Jul 2017, Genova, Italy. pp.308 - 314, ⟨10.1109/HPCS.2017.55⟩. ⟨hal-01591466⟩

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