Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields

Louis Lagardère (1) , Luc-Henri Jolly (2) , Filippo Lipparini (3) , Félix Aviat (4) , Benjamin Stamm (5) , Zhifeng F Jing (6) , Matthew Harger (6) , Hedieh Torabifard (7) , G. Andrés Cisneros (8) , Michael Schnieders (9) , Nohad Gresh (4) , Yvon Maday (10) , Pengyu Ren (11) , Jay W Ponder (12) , Jean-Philip Piquemal (4)

1 ISCD - Institut des Sciences du Calcul et des Données
2 IP2CT - Institut Parisien de Chimie Physique et Théorique
3 Dipartimento di Chimica e Chimica Industriale
4 LCT - Laboratoire de chimie théorique
5 RWTH - Rheinisch-Westfälische Technische Hochschule Aachen University
6 Biomedical Engineering Department
7 Wayne State University [Detroit]
8 UNT - University of North Texas
9 University of Iowa [Iowa City]
10 LJLL - Laboratoire Jacques-Louis Lions
11 Biomedical Engineering [Austin]
12 WUSTL - Washington University in Saint Louis

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.

Mots clés: Polarizable force field AMOEBA; Molecular dynamics method; High performance computing; Applied mathematics; Molecular simulations; Molecular dynamics simulations; Krylov solvers; Polarizable force fields; High performance computing HPC; Force fields

Domaines: Chimie théorique et/ou physique; Modélisation et simulation; Matière Molle [cond-mat.soft]

Louis Lagardère, Luc-Henri Jolly, Filippo Lipparini, Félix Aviat, Benjamin Stamm, et al.. Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields. Chemical Science, 2018, 9, pp.956-972 ⟨10.1039/C7SC04531J⟩. ⟨hal-01648245v3⟩