Evidence map›Paper›PMID 41061220›Full record

ArticleThe journal of physical chemistry. B2025

Optimization of Lennard-Jones Parameters for Induced Dipole Polarizable Gaussian Multipole Force Field.

Taoyu Niu, Junmei Wang, Zhen Huang, Ray Luo, Piotr Cieplak, Yong Duan

Abstract read
In one paragraph

Article in The journal of physical chemistry. B, 2025. 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

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

6 authors.

Taoyu NiuDepartment of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.ORCID 0009-0004-2214-1397
Junmei WangDepartment of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.ORCID 0000-0002-9607-8229
Zhen HuangDepartments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.ORCID 0009-0003-4478-8477
Ray LuoDepartments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.ORCID 0000-0002-6346-8271
Piotr CieplakSBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States.ORCID 0000-0003-0700-5691
Yong DuanUC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.ORCID 0000-0003-3793-5099

Funding

New Generation of General AMBER Force Field for Biomedical ResearchR01GM147673 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI WANG, JUNMEI, YANG, WEI · 2022 to 2025
$1.5M
AI-Powered Biased Ligand DesignR01GM149705 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Junmei Wang · 2023 to 2026
$1.3M
NIGMS NIH HHS R01 GM147673NIGMS NIH HHS R01 GM149705
6 · The paper itself

Abstract

The van der Waals potential is an integral component in molecular mechanics force fields. In this work, we document our effort to develop the parameters for the Lennard-Jones (LJ) 12-6 potential as part of our effort to develop a polarizable Gaussian multipole force field. Starting from the GAFF2 van der Waals parameter set, atom types were assigned using the Antechamber program in the AMBER24 simulation package. Atomic charges and permanent dipoles were calculated via PCMRESP, based on electrostatic potentials computed at the MP2/aug-cc-pVTZ//MP2/6-311++G(d,p) level in four solvents with dielectric constants ranging from 4.24 to 78.36. The optimization of the LJ parameters was conducted in two stages. In the first stage, we employed CCSD(T)/CBS interaction energies of about 4.6 million dimer conformations, including those from Shaw and co-workers, and applied an iterative least-squares fitting procedure. This reduced the Boltzmann factor-weighted root-mean-square error (RMSE) from 2.44 to 0.97 kcal/mol. When tested on 161 neat liquids, the simulated densities yielded an average unsigned percent error of 5.3% from the experimental values. In the second stage, the parameters were further refined by comparing simulated and experimental densities of the same 161-liquid training set using a gradient-guided iterative search based on short molecular dynamics simulations. After 24 iterations, the average unsigned percent error was reduced to 1.71%. Extended 10 ns simulations yielded an average unsigned percent error of 1.69% for the training set densities, which compares favorably with the 2.45% error obtained from GAFF2. The RMSE for heats of vaporization (

Identifiers

PMID41061220
PMCPMC12990155

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