Evidence map›Paper›PMID 39841123›Full record

ArticleThe journal of physical chemistry letters2025

Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field.

Xiaojing Teng, Wenbo Yu, Alexander D MacKerell

Abstract read
In one paragraph

Article in The journal of physical chemistry letters, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
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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

3 authors.

Xiaojing TengUniversity of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States.
Wenbo YuUniversity of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States.ORCID 0000-0001-6962-5314
Alexander D MacKerellUniversity of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States.ORCID 0000-0001-8287-6804

Funding

Macromolecular Conformational HeterogeneityR35GM131710 · NIGMS · UNIVERSITY OF MARYLAND BALTIMORE · PI ALEXANDER D MACKERELL · 2019 to 2026
$6.2M
NIGMS NIH HHS R35 GM131710
6 · The paper itself

Abstract

An improvement in the computational efficiency of polarizable force field simulations is made through the development of a polarizable Drude water model, SWM3, in combination with the use of Lennard-Jones Particle Mesh Ewald (LJPME) for the treatment of long-range LJ interactions. The experimental bulk properties, density, heat of vaporization, dielectric constant, and self-diffusion constant of the SWM3 model are accurately replicated at ambient condition. The temperature dependence of the bulk properties is also captured except for the density. Microscopic properties, such as hydration free energy, dimer properties, and binding energies of clusters are well represented. The SWM3 model is ∼40% faster than the SWM4 water model traditionally used with the Drude force field, and use of LJPME offers an additional 30% speedup in heterogeneous systems. This combination makes the SWM3-based Drude model only 2.6-fold slower than the TIP3P-based additive simulations.

Identifiers

PMID39841123
PMCPMC11895599

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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.