Evidence map›Paper›PMID 35533269›Full record

ArticleJournal of chemical theory and computation2022

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.

Simon Boothroyd, Owen C Madin, David L Mobley, Lee-Ping Wang, John D Chodera, Michael R Shirts

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

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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

6 authors.

Simon BoothroydBoothroyd Scientific Consulting Ltd., 71-75 Shelton Street, London WC2H 9JQ, Greater London, U.K.
Owen C MadinDepartment of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States.ORCID 0000-0002-6736-3442
David L MobleyDepartment of Chemistry, University of California, Irvine, California 92617, United States.
Lee-Ping WangDepartment of Chemistry, University of California, Davis, California 95616, United States.ORCID 0000-0003-3072-9946
John D ChoderaComputational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.ORCID 0000-0003-0542-119X
Michael R ShirtsDepartment of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States.ORCID 0000-0003-3249-1097

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4M
Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug designR01GM132386 · NIGMS · UNIVERSITY OF COLORADO · PI SHIRTS, MICHAEL R · 2020 to 2023
$3.1M
NCI NIH HHS P30 CA008748NIGMS NIH HHS R01 GM132386
6 · The paper itself

Abstract

Developing a sufficiently accurate classical force field representation of molecules is key to realizing the full potential of molecular simulations as a route to gaining a fundamental insight into a broad spectrum of chemical and biological phenomena. This is only possible, however, if the many complex interactions between molecules of different species in the system are accurately captured by the model. Historically, the intermolecular van der Waals (vdW) interactions have primarily been trained against densities and enthalpies of vaporization of pure (single-component) systems, with occasional usage of hydration free energies. In this study, we demonstrate how including physical property data of binary mixtures can better inform these parameters, encoding more information about the underlying physics of the system in complex chemical mixtures. To demonstrate this, we retrain a select number of Lennard-Jones parameters describing the vdW interactions of the OpenFF 1.0.0 (Parsley) fixed charge force field against training sets composed of densities and enthalpies of mixing for binary liquid mixtures as well as densities and enthalpies of vaporization of pure liquid systems and assess the performance of each of these combinations. We show that retraining against the mixture data improves the force field's ability to reproduce mixture properties, including solvation free energies, correcting some systematic errors that exist when training vdW interactions against properties of pure systems only.

Indexed as

Thermodynamics

Identifiers

PMID35533269
PMCPMC9254460

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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.