Evidence map›Paper›PMID 31176325›Full record

ArticleThe Journal of chemical physics2019

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation.

Xiongwu Wu, Bernard R Brooks

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2019. 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. Isotropic Periodic Sum for Polarizable Gaussian Multipole Model.Journal of chemical theory and computation · 2025
    Article
  3. Review
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

2 authors.

Xiongwu WuLaboratory of Computational Biology, NHLBI, NIH, 12 South Dr., Bldg. 12A, Room 3053K, Bethesda, Maryland 20892, USA.ORCID 0000000298837241
Bernard R BrooksLaboratory of Computational Biology, NHLBI, NIH, 12 South Dr., Bldg. 12A, Room 3053K, Bethesda, Maryland 20892, USA.ORCID 0000000235862730

Funding

Development Of Theoretical Methods For Studying Biological MacromoleculesZIAHL001051 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI BROOKS, BERNARD R · 2009 to 2025
$16.2M
THREE-DIMENSIONAL STRUCTURES OF BIOLOGICAL MACROMOLECULESZ01HL001027 · NHLBI · NATIONAL HEART, LUNG, AND BLOOD INSTITUTE · PI BROOKS, BERNARD R · 1985 to 2008
$617k
Intramural NIH HHS Z01 HL001027
6 · The paper itself

Abstract

Isotropic periodic sum (IPS) is a method to calculate long-range interactions based on the homogeneity of simulation systems. By using the isotropic periodic images of a local region to represent remote structures, long-range interactions become a function of the local conformation. This function is called the IPS potential, which folds long-ranged interactions into a short-ranged potential and can be calculated as efficiently as a cutoff method. Analytic solutions of IPS potentials have been solved for many interaction types. To further simplify the application of the IPS method, this work presents the homogeneity condition, which requires the sum of interaction energies for any particle to be independent of cutoff distances for a truly homogeneous system. Using the homogeneity condition, one can avoid the complicated mathematic work to solve analytic solutions and can instead use simple functions as IPS potentials. Example simulations are performed for model systems of a series of interaction types. Energies, volumes, and their fluctuations from these simulations demonstrate that simple IPS potentials obtained through the homogeneity condition can satisfactorily describe long-range interactions. The homogeneity condition makes the IPS method a convenient way to handle long-range interactions of any type.

Identifiers

PMID31176325
PMCPMC6551215

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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.