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An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

[Image: see text] Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are...

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Autores principales: Kříž, Kristian, Schmidt, Lisa, Andersson, Alfred T., Walz, Marie-Madeleine, van der Spoel, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9875315/
https://www.ncbi.nlm.nih.gov/pubmed/36630710
http://dx.doi.org/10.1021/acs.jcim.2c01127
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author Kříž, Kristian
Schmidt, Lisa
Andersson, Alfred T.
Walz, Marie-Madeleine
van der Spoel, David
author_facet Kříž, Kristian
Schmidt, Lisa
Andersson, Alfred T.
Walz, Marie-Madeleine
van der Spoel, David
author_sort Kříž, Kristian
collection PubMed
description [Image: see text] Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.
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spelling pubmed-98753152023-01-26 An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation Kříž, Kristian Schmidt, Lisa Andersson, Alfred T. Walz, Marie-Madeleine van der Spoel, David J Chem Inf Model [Image: see text] Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force. American Chemical Society 2023-01-11 /pmc/articles/PMC9875315/ /pubmed/36630710 http://dx.doi.org/10.1021/acs.jcim.2c01127 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Kříž, Kristian
Schmidt, Lisa
Andersson, Alfred T.
Walz, Marie-Madeleine
van der Spoel, David
An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
title An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
title_full An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
title_fullStr An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
title_full_unstemmed An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
title_short An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
title_sort imbalance in the force: the need for standardized benchmarks for molecular simulation
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9875315/
https://www.ncbi.nlm.nih.gov/pubmed/36630710
http://dx.doi.org/10.1021/acs.jcim.2c01127
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