Cargando…

Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations

[Image: see text] We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradie...

Descripción completa

Detalles Bibliográficos
Autores principales: Aviat, Félix, Levitt, Antoine, Stamm, Benjamin, Maday, Yvon, Ren, Pengyu, Ponder, Jay W., Lagardère, Louis, Piquemal, Jean-Philip
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2016
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5228058/
https://www.ncbi.nlm.nih.gov/pubmed/28068773
http://dx.doi.org/10.1021/acs.jctc.6b00981
_version_ 1782493914083622912
author Aviat, Félix
Levitt, Antoine
Stamm, Benjamin
Maday, Yvon
Ren, Pengyu
Ponder, Jay W.
Lagardère, Louis
Piquemal, Jean-Philip
author_facet Aviat, Félix
Levitt, Antoine
Stamm, Benjamin
Maday, Yvon
Ren, Pengyu
Ponder, Jay W.
Lagardère, Louis
Piquemal, Jean-Philip
author_sort Aviat, Félix
collection PubMed
description [Image: see text] We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration (“peek”), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter ω, can be made at almost no cost. This method is denoted by TCG-n(ω). Black-box adaptive methods to find good choices of ω are provided and discussed. Results show that TPCG-3(ω) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(ω) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production algorithm. The T(P)CG-1(ω) level provides less accurate solutions for inhomogeneous systems, but its applicability to well-conditioned problems such as water is remarkable, with only two matrix-vector product evaluations.
format Online
Article
Text
id pubmed-5228058
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher American Chemical Society
record_format MEDLINE/PubMed
spelling pubmed-52280582017-01-15 Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations Aviat, Félix Levitt, Antoine Stamm, Benjamin Maday, Yvon Ren, Pengyu Ponder, Jay W. Lagardère, Louis Piquemal, Jean-Philip J Chem Theory Comput [Image: see text] We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration (“peek”), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter ω, can be made at almost no cost. This method is denoted by TCG-n(ω). Black-box adaptive methods to find good choices of ω are provided and discussed. Results show that TPCG-3(ω) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(ω) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production algorithm. The T(P)CG-1(ω) level provides less accurate solutions for inhomogeneous systems, but its applicability to well-conditioned problems such as water is remarkable, with only two matrix-vector product evaluations. American Chemical Society 2016-11-22 2017-01-10 /pmc/articles/PMC5228058/ /pubmed/28068773 http://dx.doi.org/10.1021/acs.jctc.6b00981 Text en Copyright © 2016 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Aviat, Félix
Levitt, Antoine
Stamm, Benjamin
Maday, Yvon
Ren, Pengyu
Ponder, Jay W.
Lagardère, Louis
Piquemal, Jean-Philip
Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
title Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
title_full Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
title_fullStr Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
title_full_unstemmed Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
title_short Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
title_sort truncated conjugate gradient: an optimal strategy for the analytical evaluation of the many-body polarization energy and forces in molecular simulations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5228058/
https://www.ncbi.nlm.nih.gov/pubmed/28068773
http://dx.doi.org/10.1021/acs.jctc.6b00981
work_keys_str_mv AT aviatfelix truncatedconjugategradientanoptimalstrategyfortheanalyticalevaluationofthemanybodypolarizationenergyandforcesinmolecularsimulations
AT levittantoine truncatedconjugategradientanoptimalstrategyfortheanalyticalevaluationofthemanybodypolarizationenergyandforcesinmolecularsimulations
AT stammbenjamin truncatedconjugategradientanoptimalstrategyfortheanalyticalevaluationofthemanybodypolarizationenergyandforcesinmolecularsimulations
AT madayyvon truncatedconjugategradientanoptimalstrategyfortheanalyticalevaluationofthemanybodypolarizationenergyandforcesinmolecularsimulations
AT renpengyu truncatedconjugategradientanoptimalstrategyfortheanalyticalevaluationofthemanybodypolarizationenergyandforcesinmolecularsimulations
AT ponderjayw truncatedconjugategradientanoptimalstrategyfortheanalyticalevaluationofthemanybodypolarizationenergyandforcesinmolecularsimulations
AT lagarderelouis truncatedconjugategradientanoptimalstrategyfortheanalyticalevaluationofthemanybodypolarizationenergyandforcesinmolecularsimulations
AT piquemaljeanphilip truncatedconjugategradientanoptimalstrategyfortheanalyticalevaluationofthemanybodypolarizationenergyandforcesinmolecularsimulations