Evidence map›Paper›PMID 27802661›Full record

ArticleThe Journal of chemical physics2016

An empirical extrapolation scheme for efficient treatment of induced dipoles.

Andrew C Simmonett, Frank C Pickard, Jay W Ponder, Bernard R Brooks

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2016. 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. Review
  3. A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics.Journal of chemical theory and computation · 2024
    Article
  4. Article
  5. Article
  6. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.Journal of chemical theory and computation · 2021
    Article
  7. Article
  8. Article
  9. Drude Polarizable Force Field Parametrization of Carboxylate andJournal of chemical theory and computation · 2019
    Article
  10. Review
  11. Review
  12. Force Fields for Small Molecules.Methods in molecular biology (Clifton, N.J.) · 2019
    Article
  13. Tinker 8: Software Tools for Molecular Design.Journal of chemical theory and computation · 2018
    Article
  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

4 authors.

Andrew C SimmonettLaboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Frank C PickardLaboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Jay W PonderDepartment of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA.
Bernard R BrooksLaboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

Funding

Development Of Theoretical Methods For Studying Biological MacromoleculesZIAHL001051 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI BROOKS, BERNARD R · 2009 to 2025
$16.2M
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

Many cutting edge force fields include polarization, to enhance their accuracy and range of applicability. In this work, we develop efficient strategies for the induced dipole polarization method. By fitting various orders of perturbation theory (PT) dipoles to a diverse training set, we arrive at a family of fully analytic methods - whose nth order is referred to OPTn - that span the full spectrum of polarization methods from the fast zeroth-order approach that neglects mutual dipole coupling, approaching the fully variational approach at high order. Our training set contains many difficult cases where the PT series diverges, and we demonstrate that our OPTn methods still deliver excellent results in these cases. Our tests show that the OPTn methods exhibit rapid convergence towards the exact answer with each increasing PT order. The fourth order OPT4 method, whose costs are commensurate with three iterations of the leading conjugate gradient method, is a particularly promising candidate to be used as a drop-in replacement for existing solvers without further parameterization.

Identifiers

PMID27802661
PMCPMC5085973

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.