Evidence map›Paper›PMID 35507313›Full record

ArticleJournal of chemical theory and computation2022

Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation.

Simon Boothroyd, Lee-Ping Wang, David L Mobley, 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 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. Article
  3. Article
  4. Article
  5. Reversible molecular simulation for training classical and machine-learning force fields.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  6. Article
  7. Article
  8. Review
  9. A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics.Journal of chemical theory and computation · 2024
    Article
  10. Tuning Potential Functions to Host-Guest Binding Data.Journal of chemical theory and computation · 2024
    Article
  11. Article
  12. Article
  13. 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

5 authors.

Simon BoothroydComputational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.ORCID 0000-0002-3456-1872
Lee-Ping WangDepartment of Chemistry, The University of California at Davis, Davis, California 95616, United States.ORCID 0000-0003-3072-9946
David L MobleyDepartments of Pharmaceutical Sciences and Chemistry, The University of California at Irvine, Irvine, California 92617, United States.ORCID 0000-0002-1083-5533
John D ChoderaComputational and 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 accurate classical force field representations of molecules is key to realizing the full potential of molecular simulations, both as a powerful route to gaining fundamental insights into a broad spectrum of chemical and biological phenomena and for predicting physicochemical and mechanical properties of substances. The Open Force Field Consortium is an industry-funded open science effort to this end, developing open-source tools for rapidly generating new high-quality small-molecule force fields. An integral aspect of this is the parameterization and assessment of force fields against high-quality, condensed-phase physical property data, curated from open data sources such as the NIST ThermoML Archive, alongside quantum chemical data. The quantity of such experimental data in open data archives alone would require an onerous amount of human and computational resources to both curate and estimate manually, especially when estimations must be obtained for numerous sets of force field parameters. Here, we present an entirely automated, highly scalable framework for evaluating physical properties and their gradients in terms of force field parameters. It is written as a modular and extensible Python framework, which employs an intelligent multiscale estimation approach that allows for the automated estimation of properties from simulation and cached simulation data, and a pluggable API for estimation of new properties. In this study, we demonstrate the utility of the framework by benchmarking the OpenFF 1.0.0 small-molecule force field and GAFF 1.8 and GAFF 2.1 force fields against a test set of binary density and enthalpy of mixing measurements curated using the framework utilities. Further, we demonstrate the framework's utility as part of force field optimization by using it alongside ForceBalance, a framework for systematic force field optimization, to retrain a set of nonbonded van der Waals parameters against a training set of density and enthalpy of vaporization measurements.

Indexed as

ThermodynamicsComputer SimulationHumans

Identifiers

PMID35507313
PMCPMC9245177

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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.