Evidence map›Paper›PMID 42639997›Full record

ArticleThe Journal of chemical physics2026

Precomputed grid potential (PGP) method: Exact reciprocal-space acceleration of particle mesh Ewald for Monte Carlo simulations.

Mingtian Zhao, Wenbo Yu, Alexander D MacKerell

Abstract read
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Article in The Journal of chemical physics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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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

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3 · Its place in the literature

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0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Mingtian ZhaoComputer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn St., Baltimore, Maryland 21201, USA.ORCID 0009-0006-7068-6927
Wenbo YuComputer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn St., Baltimore, Maryland 21201, USA.ORCID 0000-0001-6962-5314
Alexander D MacKerellComputer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn St., Baltimore, Maryland 21201, USA.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

When conducting Monte Carlo (MC) simulations using a fixed or infrequently updated charge environment, each insertion or deletion of a particle requires an O(N log N) particle mesh Ewald (PME) long-range electrostatics calculation. To address this, we have developed Precomputed Grid Potential (PGP). This approach is a mathematically exact redesign of the smoothed PME (SPME) stationary-mobile reciprocal cross-term, which has an O(1) reciprocal-space cost in the stationary region size per insertion and achieves no loss of accuracy when compared to the discrete SPME calculation using the same mesh. After precomputing the static contribution of the stationary charges on a 3D grid employing a B-spline interpolation operator, particle insertions only require O(1) interpolations of the stationary potential and not a Fourier transform. The PGP and PME cross-terms are algebraically the same, and the only source of numerical variation between them is the position-dependent mesh self-artifact included in discrete PME. This is eliminated by construction in PGP's cross-term formulation. We have compared PGP to PME for water sampling in protein systems of up to 56K atoms, showing through grand canonical Monte Carlo (GCMC) simulations that, after independent calibration of the chemical potential, all distribution measurements, including mean occupancy and interaction energy, were statistically indistinguishable, while accept/reject ratios differed by no more than 0.23%. For these fixed-stationary region GCMC workloads, PGP reduces the per-trial reciprocal-space cost (4678× to 9857×) at an identical SPME Hamiltonian, mesh size, and order of B-spline.

Identifiers

PMID42639997
PMCPMC13539627

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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.