Evidence map›Paper›PMID 41324183›Full record

ArticleThe Journal of chemical physics2025

Mass-zero constrained molecular dynamics for electrostatic interactions.

Federica Troni, Davide Grassano, Jayashree Narayan, Benoît Roux, Sara Bonella

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Federica TroniCentre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.ORCID 0009-0005-4454-2404
Davide GrassanoCentre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.ORCID 0000-0001-8821-6452
Jayashree NarayanCentre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.ORCID 0009-0007-8280-1010
Benoît RouxDepartment of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000-0002-5254-2712
Sara BonellaCentre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.ORCID 0000-0003-4131-2513

Funding

Molecular dynamics studies of K+ and Na+ channels and biomembranes based on a polarizable force fieldR35GM152124 · NIGMS · UNIVERSITY OF CHICAGO · PI BENOIT ROUX · 2024 to 2026
$2.2M
NIGMS NIH HHS R35 GM152124
6 · The paper itself

Abstract

Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most efficient methods are currently based on particle-mesh Ewald sums and achieve semi-logarithmic scaling in the number of particles. These methods solve the problem in reciprocal space, requiring extensive use of fast Fourier transforms. While highly efficient in many contexts, FFTs may encounter scalability challenges at very large processor counts due to their communication requirements. To mitigate these problems, the development and scalable coding of real-space approaches to solve the Poisson equation on a grid is an active field of research. In this work, we introduce a novel real-space approach that provides some advantages over alternatives. Our method exploits an extended Lagrangian in which the values of the field at the grid points are treated as auxiliary variables of zero inertia and the discretized Poisson equation is enforced as a dynamical constraint. The solution of the constraints leads to a linear system-different from those appearing in other real-space approaches-that can be efficiently solved via state-of-the-art iterative methods. The method inherits the numerical scaling of the adopted iterative solver, e.g., linear with a multigrid approach, but converges with fewer cycles. We analyze this approach considering realistic simulations of molten NaCl that validate its ability to reproduce structural and transport properties. Using this non-trivial benchmark, we demonstrate linear scaling and illustrate some features of our algorithm.

Identifiers

PMID41324183
PMCPMC12742476

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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.