title: Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald.
abstract: In this article, we present a parallel implementation of point dipole-based polarizable force fields for molecular dynamics (MD) simulations with periodic boundary conditions (PBC). The smooth particle mesh Ewald technique is combined with two optimal iterative strategies, namely, a preconditioned conjugate gradient solver and a Jacobi solver in conjunction with the direct inversion in the iterative subspace for convergence acceleration, to solve the polarization equations. We show that both solvers exhibit very good parallel performances and overall very competitive timings in an energy and force computation needed to perform a MD step. Various tests on large systems are provided in the context of the polarizable AMOEBA force field as implemented in the newly developed Tinker-HP package, which is the first implementation of a polarizable model that makes large-scale experiments for massively parallel PBC point dipole models possible. We show that using a large number of cores offers a significant acceleration of the overall process involving the iterative methods within the context of SPME and a noticeable improvement of the memory management, giving access to very large systems (hundreds of thousands of atoms) as the algorithm naturally distributes the data on different cores. Coupled with advanced MD techniques, gains ranging from 2 to 3 orders of magnitude in time are now possible compared to nonoptimized, sequential implementations, giving new directions for polarizable molecular dynamics with periodic boundary conditions using massively parallel implementations.
authors.affiliation: Institut du Calcul et de la Simulation, UPMC Univ. Paris 06 , F-75005, Paris, France.|Laboratoire de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617 , F-75005, Paris, France.
authors.forename: Louis
authors.initials: L
authors.lastname: Lagardère
authors.affiliation: Institut du Calcul et de la Simulation, UPMC Univ. Paris 06 , F-75005, Paris, France.|Laboratoire de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617 , F-75005, Paris, France.|Laboratoire Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598 , F-75005, Paris, France.
authors.forename: Filippo
authors.initials: F
authors.lastname: Lipparini
authors.affiliation: Laboratoire de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617 , F-75005, Paris, France.|Laboratoire Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598 , F-75005, Paris, France.
authors.forename: Étienne
authors.initials: É
authors.lastname: Polack
authors.affiliation: Laboratoire Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598 , F-75005, Paris, France.|CNRS, UMR 7598 and 7616 , F-75005, Paris, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Stamm
authors.affiliation: Université Paris-Est, CERMICS, Ecole des Ponts and INRIA , 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée, France.
authors.forename: Éric
authors.initials: É
authors.lastname: Cancès
authors.affiliation: Departments of Biomedical Engineering and Biochemistry, The University of Iowa , Iowa City, Iowa 52358, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Schnieders
authors.affiliation: Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States.
authors.forename: Pengyu
authors.initials: P
authors.lastname: Ren
authors.affiliation: Laboratoire Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598 , F-75005, Paris, France.|Institut Universitaire de France , F-75005, Paris, France.|Division of Applied Mathematics, Brown University , Providence, Rhode Island 02912, United States.
authors.forename: Yvon
authors.initials: Y
authors.lastname: Maday
authors.affiliation: Laboratoire de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617 , F-75005, Paris, France.
authors.forename: Jean-Philip
authors.initials: JP
authors.lastname: Piquemal
mesh_terms: D056004:Molecular Dynamics Simulation; D010316:Particle Size; D013499:Surface Properties