Evidence map›Paper›PMID 36630710›Full record

ReviewJournal of chemical information and modeling2023

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

Kristian Kříž, Lisa Schmidt, Alfred T Andersson, Marie-Madeleine Walz, David van der Spoel

Abstract readReview
In one paragraph

Review in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Article
  2. Article
  3. Uncertainty Quantification forChemical reviews · 2026
    Review
  4. Article
  5. Review
  6. Article
  7. gmXtal: Cooking Crystals with GROMACS.The protein journal · 2024
    Article
  8. Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?The journal of physical chemistry letters · 2024
    Article
  9. 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.

Kristian KřížDepartment of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden.ORCID 0000-0001-9072-0949
Lisa SchmidtFaculty of Biosciences, University of Heidelberg, Heidelberg69117, Germany.ORCID 0000-0001-7058-3107
Alfred T AnderssonDepartment of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden.ORCID 0000-0002-6101-4823
Marie-Madeleine WalzDepartment of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden.ORCID 0000-0002-3932-5780
David van der SpoelDepartment of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden.ORCID 0000-0002-7659-8526

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

Artificial IntelligenceComputer SimulationIonsIons

Identifiers

PMID36630710
PMCPMC9875315

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.