Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

Louis Lagardère; Luc-Henri Jolly; Filippo Lipparini; Félix Aviat; Benjamin Stamm; Zhifeng F Jing; Matthew Harger; Hedieh Torabifard; G. Andrés Cisneros; Michael J Schnieders; Nohad Gresh; Yvon Maday; Pengyu Y Ren; Jay W Ponder; Jean-Philip Piquemal

doi:10.1039/C7SC04531J

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Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

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Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

Louis Lagardère, Luc-Henri Jolly, Filippo Lipparini, Félix Aviat, Benjamin Stamm, Zhifeng F Jing, Matthew Harger, Hedieh Torabifard, G. Andrés Cisneros, Michael J Schnieders, …

Chemical science (Cambridge), Vol.9(4), pp.956-972

2018

DOI: 10.1039/C7SC04531J

PMID: 29732110

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Abstract

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.

Details

Title: Subtitle: Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
Creators: Louis Lagardère - Sorbonne Université, Institut des Sciences du Calcul et des Données, Paris, France, Sorbonne Université
Luc-Henri Jolly - Sorbonne Université, Institut Parisien de Chimie Physique et Théorique, CNRS, Paris, France
Filippo Lipparini - Universita di Pisa, Dipartimento di Chimica e Chimica Industriale, Pisa, Italy
Félix Aviat - Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616, CNRS, Paris
Benjamin Stamm - MATHCCES, Department of Mathematics, RWTH Aachen University, Aachen, Germany
Zhifeng F Jing - The University of Texas at Austin, Department of Biomedical Engineering, USA
Matthew Harger - The University of Texas at Austin, Department of Biomedical Engineering, USA
Hedieh Torabifard - Department of Chemistry, Wayne State University, Detroit, USA
G. Andrés Cisneros - Department of Chemistry, University of North Texas, Denton, USA
Michael J Schnieders - The University of Iowa, Department of Biomedical Engineering, Iowa City, USA
Nohad Gresh - Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616, CNRS, Paris
Yvon Maday - Sorbonne Université, Laboratoire Jacques-Louis Lions, UMR 7598, CNRS, Paris
Pengyu Y Ren - The University of Texas at Austin, Department of Biomedical Engineering, USA
Jay W Ponder - Washington University in Saint Louis, Department of Chemistry, Saint Louis, USA
Jean-Philip Piquemal - Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616, CNRS, Paris
Resource Type: Journal article
Publication Details: Chemical science (Cambridge), Vol.9(4), pp.956-972
DOI: 10.1039/C7SC04531J
PMID: 29732110
NLM abbreviation: Chem Sci
ISSN: 2041-6520
eISSN: 2041-6539
Grant note: DOI: 10.13039/100000052, name: NIH Office of the Director, award: R01GM106137 and R01GM114237; DOI: 10.13039/100000001, name: National Science Foundation, award: DGE-1610403; DOI: 10.13039/501100004794, name: Centre National de la Recherche Scientifique, award: PICS international collaboration grant (Sorbonne U.-UT AUstin); DOI: 10.13039/501100001665, name: Agence Nationale de la Recherche, award: ANR11-IDEX-0004-02
Language: English
Date published: 2018
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
Record Identifier: 9984025278602771

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