title: Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.
abstract: In this paper, we present a scalable and efficient 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-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 for a polarizable model making 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 non-optimized, sequential implementations giving new directions for polarizable molecular dynamics in periodic boundary conditions using massively parallel implementations.
authors.affiliation: UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France.
authors.forename: Louis
authors.initials: L
authors.lastname: Lagardère
authors.affiliation: UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France ; UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France.
authors.forename: Filippo
authors.initials: F
authors.lastname: Lipparini
authors.affiliation: UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France.
authors.forename: Étienne
authors.initials: É
authors.lastname: Polack
authors.affiliation: UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, 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: UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; Institut Universitaire de France ; Brown Univ, Division of Applied Maths, Providence, RI, USA.
authors.forename: Yvon
authors.initials: Y
authors.lastname: Maday
authors.affiliation: UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France.
authors.forename: Jean-Philip
authors.initials: JP
authors.lastname: Piquemal