Evidence map›Paper›PMID 28068773›Full record

ArticleJournal of chemical theory and computation2017

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

Félix Aviat, Antoine Levitt, Benjamin Stamm, Yvon Maday, Pengyu Ren, Jay W Ponder, Louis Lagardère, Jean-Philip Piquemal

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Article
  2. Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models.Journal of chemical theory and computation · 2023
    Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.Journal of chemical theory and computation · 2021
    Article
  8. Article
  9. Article
  10. Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019
    Article
  11. Article
  12. Review
  13. Review
  14. Article
  15. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Félix AviatLaboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.
Antoine LevittInria Paris, F-75589 Paris Cedex 12, Université Paris-Est, CERMICS (ENPC) , Marne-la-Vallée, F-77455, France.
Benjamin StammMATHCCES, Department of Mathematics, RWTH Aachen University , Schinkelstraße 2, D-52062 Aachen, Germany.
Yvon MadayLaboratoire Jacques-Louis Lions, UPMC Université Paris 06, UMR 7598 , F-75005, Paris, France.
Pengyu RenDepartment of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States.
Jay W PonderDepartment of Chemistry, Washington University in Saint Louis , Campus Box 1134, One Brookings Drive, Saint Louis, Missouri 63130, United States.
Louis LagardèreLaboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.
Jean-Philip PiquemalLaboratoire de Chimie Théorique, UPMC Université Paris 06, UMR 7617 , F-75005, Paris, France.ORCID 0000-0001-6615-9426

Funding

DEVELOPMENT OF A NEXT-GENERATION NUCLEIC ACID FORCE FIELDR01GM106137 · NIGMS · WASHINGTON UNIVERSITY · PI JAY PONDER, Pengyu Ren · 2013 to 2026
$3.5M
Specificity and Selectivity in Protein-Ion BindingR01GM114237 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI PONDER, JAY, REN, PENGYU · 2015 to 2023
$2.6M
NIGMS NIH HHS R01 GM106137NIGMS NIH HHS R01 GM114237
6 · The paper itself

Abstract

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.

Indexed as

Molecular Dynamics SimulationThermodynamicsAlgorithmsMonte Carlo Method

Identifiers

PMID28068773
PMCPMC5228058

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.