Journal article
Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald
Journal of chemical theory and computation, Vol.11(6), pp.2589-2599
06/09/2015
DOI: 10.1021/acs.jctc.5b00171
PMID: 26575557
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.
Details
- Title: Subtitle
- Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: II. Toward massively parallel computations using smooth particle mesh Ewald
- Creators
- Louis Lagardère - Laboratoire de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617 , F-75005, Paris, FranceFilippo Lipparini - Laboratoire Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598 , F-75005, Paris, FranceÉtienne Polack - Laboratoire Jacques-Louis Lions, UPMC Univ. Paris 06, UMR 7598 , F-75005, Paris, FranceBenjamin Stamm - CNRS, UMR 7598 and 7616 , F-75005, Paris, FranceÉric Cancès - Université Paris-Est, CERMICS, Ecole des Ponts and INRIA , 6 & 8 avenue Blaise Pascal, 77455 Marne-la-Vallée, FranceMichael Schnieders - Departments of Biomedical Engineering and Biochemistry, The University of Iowa , Iowa City, Iowa 52358, United StatesPengyu Ren - Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United StatesYvon Maday - Division of Applied Mathematics, Brown University , Providence, Rhode Island 02912, United StatesJean-Philip Piquemal - Laboratoire de Chimie Théorique, UPMC Univ. Paris 06, UMR 7617 , F-75005, Paris, France
- Resource Type
- Journal article
- Publication Details
- Journal of chemical theory and computation, Vol.11(6), pp.2589-2599
- DOI
- 10.1021/acs.jctc.5b00171
- PMID
- 26575557
- NLM abbreviation
- J Chem Theory Comput
- ISSN
- 1549-9618
- eISSN
- 1549-9626
- Publisher
- United States
- Grant note
- GM106137 / NIGMS NIH HHS
- Language
- English
- Date published
- 06/09/2015
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984025283102771
Metrics
18 Record Views