Evidence map›Paper›PMID 27248842›Full record

ArticleThe journal of physical chemistry. B2016

Evaluation of Representations and Response Models for Polarizable Force Fields.

Amanda Li, Alexey Voronin, Andrew T Fenley, Michael K Gilson

Abstract read
In one paragraph

Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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.

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2 · The registry

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3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics.Journal of chemical theory and computation · 2024
    Article
  2. Article
  3. Article
4 · The record

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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.

Amanda LiDepartment of Bioengineering, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0419, United States.
Alexey VoroninSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States.
Andrew T FenleySkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States.
Michael K GilsonSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States.

Funding

THEORY AND MODELING OF NONCOVALENT BINDINGR01GM061300 · NIGMS · UNIVERSITY OF MD BIOTECHNOLOGY INSTITUTE · PI GILSON, MICHAEL K. · 2000 to 2021
$7.2M
NIGMS NIH HHS R01 GM061300
6 · The paper itself

Abstract

For classical simulations of condensed-phase systems, such as organic liquids and biomolecules, to achieve high accuracy, they will probably need to incorporate an accurate, efficient model of conformation-dependent electronic polarization. Thus, it is of interest to understand what determines the accuracy of a polarizable electrostatics model. This study approaches this problem by breaking polarization models down into two main components: the representation of electronic polarization and the response model used for mapping from an inducing field to the polarization within the chosen representation. Among the most common polarization representations are redistribution of atom-centered charges, such as those used in the fluctuating charge model, and atom-centered point dipoles, such as those used in a number of different polarization models. Each of these representations has been combined with one or more response models. The response model of fluctuating charge, for example, is based on the idea of electronegativity equalization in the context of changing electrostatic potentials (ESPs), whereas point-dipole representations typically use a response model based on point polarizabilities whose induced dipoles are computed based on interaction with other charges and dipoles. Here, we decouple polarization representations from their typical response models to analyze the strengths and weaknesses of various polarization approximations. First, we compare the maximal possible accuracies achievable by the charge redistribution and point-dipole model representations, by testing their ability to replicate quantum mechanical (QM) ESPs around small molecules polarized by external inducing charges. Perhaps not surprisingly, the atom-centered dipole model can yield higher accuracy. Next, we test two of the most commonly used response functions used for the point-dipole representations, self-consistent and direct (or first-order) inducible point polarizabilities, where the polarizabilities are optimized to best fit the full set of polarized QM potentials for each molecule studied. Strikingly, the induced-dipole response model markedly degrades accuracy relative to that obtainable with optimal point dipoles. In fact, the maximal accuracy achievable with this response model is even lower than that afforded by an optimal charge-redistribution representation. This means that, if coupled with a sufficiently accurate response function, the point-charge representation could outperform the standard induced-dipole model. Furthermore, although a key advantage of the point-dipole representation, relative to charge redistribution, is its ability to capture out-of-plane polarization, the inducible dipole response model causes it to be less accurate than optimal charge redistribution for out-of-plane induction of the planar nitrobenzene molecule. Thus, the widely used inducible dipole response function falls short of the full potential accuracy achievable with the point-dipole representation it employs. Additional results reported here bear on the relative accuracy of self-consistent inducible dipoles versus that of the first-order, or direct, approximation and on methods for assigning partial atomic charges for use in conjunction with inducible dipole models. In sum, these results point to the improvement of polarization response models as an important direction for future research aimed at improving the accuracy of molecular simulations.

Indexed as

Models, MolecularStatic ElectricityComputer SimulationQuantum Theory

Identifiers

PMID27248842
PMCPMC5002935

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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.