Evidence map›Paper›PMID 37747971›Full record

ArticleJournal of chemical theory and computation2023

Reducing the Cost of Neural Network Potential Generation for Reactive Molecular Systems.

Krystof Brezina, Hubert Beck, Ondrej Marsalek

Abstract read
In one paragraph

Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Prebiotic chemical reactivity in solution with quantum accuracy and microsecond sampling using neural network potentials.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  5. 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

3 authors.

Krystof BrezinaCharles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.ORCID 0000-0003-0285-1282
Hubert BeckCharles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.ORCID 0000-0002-7191-2192
Ondrej MarsalekCharles University, Faculty of Mathematics and Physics, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.ORCID 0000-0002-8624-8837

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Although machine learning potentials have recently had a substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio simulation that covers all the relevant geometries of the system. Recognizing that this can be prohibitive for certain systems, we develop the method of transition tube sampling that mitigates the computational cost of training set and model generation. In this approach, we generate classical or quantum thermal geometries around a transition path describing a conformational change or a chemical reaction using only a sparse set of local normal mode expansions along this path and select from these geometries by an active learning protocol. This yields a training set with geometries that characterize the whole transition without the need for a costly reference trajectory. The performance of the method is evaluated on different molecular systems with the complexity of the potential energy landscape increasing from a single minimum to a double proton-transfer reaction with high barriers. Our results show that the method leads to training sets that give rise to models applicable in classical and path integral simulations alike that are on par with those based directly on ab initio calculations while providing the computational speedup we have come to expect from machine learning potentials.

Identifiers

PMID37747971
PMCPMC10569056

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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.