Journal article
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations
Journal of chemical theory and computation, Vol.10(4), pp.1638-1651
02/28/2014
DOI: 10.1021/ct401096t
PMCID: PMC4620587
PMID: 26512230
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.
Details
- Title: Subtitle
- Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations
- Creators
- Louis Lagardère - 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, FranceFilippo Lipparini - 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, FranceÉtienne Polack - 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, FranceBenjamin Stamm - UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France ; 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 - 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, USAJean-Philip Piquemal - UPMC Univ. Paris 06, UMR 7617, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Resource Type
- Journal article
- Publication Details
- Journal of chemical theory and computation, Vol.10(4), pp.1638-1651
- DOI
- 10.1021/ct401096t
- PMID
- 26512230
- PMCID
- PMC4620587
- NLM abbreviation
- J Chem Theory Comput
- ISSN
- 1549-9618
- eISSN
- 1549-9626
- Publisher
- United States
- Grant note
- R01 GM106137 / NIGMS NIH HHS
- Language
- English
- Date published
- 02/28/2014
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984024555602771
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