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Journal Articles

Fast and flexible long-range models for atomistic machine learning

Open Access
Philip Loche, Kevin K. Huguenin-Dumittan, Melika Honarmand, Qianjun Xu, Egor Rumiantsev, Wei Bin How, Marcel F. Langer, Michele Ceriotti
Journal: The Journal of Chemical Physics
J. Chem. Phys. 162, 142501 (2025)
https://doi.org/10.1063/5.0251713
Published: April 2025
View articletitled, Fast and flexible long-range models for atomistic machine learning
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Journal Articles

A simple efficient algorithm for molecular simulations of constant potential electrodes

Open Access
Ranisha S. Sitlapersad, Anthony R. Thornton, Wouter K. den Otter
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 034107 (2024)
https://doi.org/10.1063/5.0171502
Published: January 2024
View articletitled, A simple efficient algorithm for molecular simulations of constant potential electrodes
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Journal Articles

ELECTRODE: An electrochemistry package for atomistic simulations

Open Access
Ludwig J. V. Ahrens-Iwers, Mathijs Janssen, Shern R. Tee, Robert H. Meißner
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 084801 (2022)
https://doi.org/10.1063/5.0099239
Published: August 2022
View articletitled, ELECTRODE: An electrochemistry package for atomistic simulations
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Includes: Supplementary data
Journal Articles

Superscalability of the random batch Ewald method

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Jiuyang Liang, Pan Tan, Yue Zhao, Lei Li, Shi Jin, Liang Hong, Zhenli Xu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 156, 014114 (2022)
https://doi.org/10.1063/5.0073424
Published: January 2022
View articletitled, Superscalability of the random batch Ewald method
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Journal Articles

Constant potential simulations on a mesh

Open Access
Ludwig J. V. Ahrens-Iwers, Robert H. Meißner
Journal: The Journal of Chemical Physics
J. Chem. Phys. 155, 104104 (2021)
https://doi.org/10.1063/5.0063381
Published: September 2021
View articletitled, Constant potential simulations on a mesh
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Includes: Supplementary data
Journal Articles

Multilevel summation for periodic electrostatics using B-splines

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Hüseyin Kaya, David J. Hardy, Robert D. Skeel
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 144105 (2021)
https://doi.org/10.1063/5.0040925
Published: April 2021
View articletitled, Multilevel summation for periodic electrostatics using B-splines
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Journal Articles

Evaluation of the work of adhesion at the interface between a surface-modified metal oxide and an organic solvent using molecular dynamics simulations

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Takamasa Saito, Eita Shoji, Masaki Kubo, Takao Tsukada, Gota Kikugawa, Donatas Surblys
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 114703 (2021)
https://doi.org/10.1063/5.0040900
Published: March 2021
View articletitled, Evaluation of the work of adhesion at the interface between a surface-modified metal oxide and an organic solvent using molecular dynamics simulations
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Includes: Supplementary data
Journal Articles

Particle–particle particle–mesh algorithm for electrolytes between charged dielectric interfaces

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Jiaxing Yuan, Hanne S. Antila, Erik Luijten
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 094115 (2021)
https://doi.org/10.1063/5.0035944
Published: March 2021
View articletitled, Particle–particle particle–mesh algorithm for electrolytes between charged dielectric interfaces
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Includes: Supplementary data
Journal Articles

A coarse-grained model of dimethyl sulfoxide for molecular dynamics simulations with lipid membranes

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Shobhna, Monika Kumari, Hemant K. Kashyap
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 035104 (2020)
https://doi.org/10.1063/5.0014614
Published: July 2020
View articletitled, A coarse-grained model of dimethyl sulfoxide for molecular dynamics simulations with lipid membranes
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Journal Articles

Harmonic surface mapping algorithm for molecular dynamics simulations of particle systems with planar dielectric interfaces

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Jiuyang Liang, Jiaxing Yuan, Erik Luijten, Zhenli Xu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 152, 134109 (2020)
https://doi.org/10.1063/5.0003293
Published: April 2020
View articletitled, Harmonic surface mapping algorithm for molecular dynamics simulations of particle systems with planar dielectric interfaces
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Journal Articles

The evolution of acidic and ionic aggregates in ionomers during microsecond simulations

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Amalie L. Frischknecht, Karen I. Winey
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 064901 (2019)
https://doi.org/10.1063/1.5085069
Published: February 2019
View articletitled, The evolution of acidic and ionic aggregates in ionomers during microsecond simulations
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Includes: Supplementary data
Journal Articles

Calculation of the water-octanol partition coefficient of cholesterol for SPC, TIP3P, and TIP4P water

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Jorge R. Espinosa, Charlie R. Wand, Carlos Vega, Eduardo Sanz, Daan Frenkel
Journal: The Journal of Chemical Physics
J. Chem. Phys. 149, 224501 (2018)
https://doi.org/10.1063/1.5054056
Published: December 2018
View articletitled, Calculation of the water-octanol partition coefficient of cholesterol for SPC, TIP3P, and TIP4P water
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Journal Articles

Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations

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Dominik Sidler, Simon Frasch, Michael Cristòfol-Clough, Sereina Riniker
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 234105 (2018)
https://doi.org/10.1063/1.5007132
Published: June 2018
View articletitled, Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations
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Includes: Supplementary data
Journal Articles

Electrostatic interactions in dissipative particle dynamics—Ewald-like formalism, error analysis, and pressure computation

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Rakesh Vaiwala, Sameer Jadhav, Rochish Thaokar
Journal: The Journal of Chemical Physics
J. Chem. Phys. 146, 124904 (2017)
https://doi.org/10.1063/1.4978809
Published: March 2017
View articletitled, Electrostatic interactions in dissipative particle dynamics—Ewald-like formalism, error analysis, and pressure computation
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Journal Articles

A generalized Ewald decomposition for screened Coulomb interactions

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Gautham Dharuman, Liam G. Stanton, James N. Glosli, Michael S. Murillo
Journal: The Journal of Chemical Physics
J. Chem. Phys. 146, 024112 (2017)
https://doi.org/10.1063/1.4973842
Published: January 2017
View articletitled, A generalized Ewald decomposition for screened Coulomb interactions
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Journal Articles

System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO2, n-alkanes, and poly(ethylene glycol) dimethyl ethers

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Othonas A. Moultos, Yong Zhang, Ioannis N. Tsimpanogiannis, Ioannis G. Economou, Edward J. Maginn
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 074109 (2016)
https://doi.org/10.1063/1.4960776
Published: August 2016
View articletitled, System-size corrections for self-diffusion coefficients calculated from molecular dynamics simulations: The case of CO2, n-alkanes, and poly(ethylene glycol) dimethyl ethers
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Includes: Supplementary data
Journal Articles

An O(N) and parallel approach to integral problems by a kernel-independent fast multipole method: Application to polarization and magnetization of interacting particles

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Xikai Jiang, Jiyuan Li, Xujun Zhao, Jian Qin, Dmitry Karpeev, Juan Hernandez-Ortiz, Juan J. de Pablo, Olle Heinonen
Journal: The Journal of Chemical Physics
J. Chem. Phys. 145, 064307 (2016)
https://doi.org/10.1063/1.4960436
Published: August 2016
View articletitled, An O(N) and parallel approach to integral problems by a kernel-independent fast multipole method: Application to polarization and magnetization of interacting particles
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Journal Articles

Labyrinthine water flow across multilayer graphene-based membranes: Molecular dynamics versus continuum predictions

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Hiroaki Yoshida, Lydéric Bocquet
Journal: The Journal of Chemical Physics
J. Chem. Phys. 144, 234701 (2016)
https://doi.org/10.1063/1.4953685
Published: June 2016
View articletitled, Labyrinthine water flow across multilayer graphene-based membranes: Molecular dynamics versus continuum predictions
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Journal Articles

Simulations of Coulomb systems with slab geometry using an efficient 3D Ewald summation method

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Alexandre P. dos Santos, Matheus Girotto, Yan Levin
Journal: The Journal of Chemical Physics
J. Chem. Phys. 144, 144103 (2016)
https://doi.org/10.1063/1.4945560
Published: April 2016
View articletitled, Simulations of Coulomb systems with slab geometry using an efficient 3D Ewald summation method
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Journal Articles

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

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David J. Hardy, Matthew A. Wolff, Jianlin Xia, Klaus Schulten, Robert D. Skeel
Journal: The Journal of Chemical Physics
J. Chem. Phys. 144, 114112 (2016)
https://doi.org/10.1063/1.4943868
Published: March 2016
View articletitled, Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations
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