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Calculating Electrostatic Interactions Using the Particle−Particle Particle−Mesh Method with Nonperiodic Long-Range Interactions

https://doi.org/10.1021/jp9518623
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inferred← citeshttps://doi.org/10.1021/jp020356sopenalex-snapshot
Dynamic Conformations of Flavin Adenine Dinucleotide: Simulated Molecular Dynamics of the Flavin Cofactor Related to the Time-Resolved Fluorescence Characteristics
inferred← citeshttps://doi.org/10.1021/jp0350924openalex-snapshot
Influence of Artificial Periodicity and Ionic Strength in Molecular Dynamics Simulations of Charged Biomolecules Employing Lattice-Sum Methods
inferred← citeshttps://doi.org/10.1021/jp046158dopenalex-snapshot
Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study
inferred← citeshttps://doi.org/10.1021/jp0507952openalex-snapshot
Molecular Dynamics Simulations of Phospholipid Bilayers: Influence of Artificial Periodicity, System Size, and Simulation Time
inferred← citeshttps://doi.org/10.1021/jp2041982openalex-snapshot
Mechanisms and Energetics for Acid Catalyzed β- d -Glucose Conversion to 5-Hydroxymethylfurfurl
inferred← citeshttps://doi.org/10.1021/jp807421aopenalex-snapshot
Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions
inferred← citeshttps://doi.org/10.1021/jp900147ropenalex-snapshot
Combined QM/MM and Classical Molecular Dynamics Study of [Ru(bpy)3]2+ in Water
inferred← citeshttps://doi.org/10.1021/jp9937757openalex-snapshot
Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation
inferred← citeshttps://doi.org/10.1038/s41467-025-61352-6openalex-snapshot
Supramolecular nanocrystalline membranes with well-aligned subnanochannels for enhanced reverse osmosis desalination
inferred← citeshttps://doi.org/10.1038/s41467-025-68131-3openalex-snapshot
Universal modulus-free transfer of scalable laser-induced graphene for electronic skins
inferred← citeshttps://doi.org/10.1038/s41529-025-00730-3openalex-snapshot
Atomistic understanding of the impact of radiation on the aqueous leaching of sodium borosilicate glass matrix
inferred← citeshttps://doi.org/10.1038/s41598-018-30364-2openalex-snapshot
A fast and accurate computational method for the linear-combination-based isotropic periodic sum
inferred← citeshttps://doi.org/10.1038/s41598-024-54214-6openalex-snapshot
Architectural design of anode materials for superior alkali-ion (Li/Na/K) batteries storage
inferred← citeshttps://doi.org/10.1038/s41598-025-99751-wopenalex-snapshot
Identification of novel TMEM16A blockers through integrated virtual screening, molecular dynamics, and experimental studies
inferred← citeshttps://doi.org/10.1039/b314656aopenalex-snapshot
Molecular dynamics simulations of lanthanide( iii ) diphenyldimethylpyridinyl–dicarboxyamide complexes in water and in methanol: evidence for both first and second sphere complexes
inferred← citeshttps://doi.org/10.1039/c3cp44606aopenalex-snapshot
Probing micro-solvation in “numbers”: the case of neutral dipeptides in water
inferred← citeshttps://doi.org/10.1039/c5ra19932hopenalex-snapshot
Investigation of graphene oxide nanosheets dispersion in water based on solubility parameters: a molecular dynamics simulation study
inferred← citeshttps://doi.org/10.1039/c6cp02194hopenalex-snapshot
Passage of TBP–uranyl complexes from aqueous–organic interface to the organic phase: insights from molecular dynamics simulation
inferred← citeshttps://doi.org/10.1039/c7ra09387jopenalex-snapshot
Metadynamics supports molecular dynamics simulation-based binding affinities of eucalyptol and beta-cyclodextrin inclusion complexes
inferred← citeshttps://doi.org/10.1039/c8cp01272eopenalex-snapshot
Thermal conductivity of ice polymorphs: a computational study
inferred← citeshttps://doi.org/10.1039/c8cp02820fopenalex-snapshot
Seawater desalination using pillared graphene as a novel nano-membrane in reverse osmosis process: nonequilibrium MD simulation study
inferred← citeshttps://doi.org/10.1039/c8cp03283aopenalex-snapshot
Towards a coarse-grained model of the peptoid backbone: the case of N , N -dimethylacetamide
inferred← citeshttps://doi.org/10.1039/c8me00039eopenalex-snapshot
Tailoring of carbon nanotubes for the adsorption of heavy metal ions: molecular dynamics and experimental investigations
inferred← citeshttps://doi.org/10.1039/c9cp00648fopenalex-snapshot
Nanoscopic insights of saline water in carbon nanotube appended filters using molecular dynamics simulations
inferred← citeshttps://doi.org/10.1039/c9cp04364kopenalex-snapshot
Breakdown of continuum model for water transport and desalination through ultrathin graphene nanopores: insights from molecular dynamics simulations
inferred← citeshttps://doi.org/10.1039/d0ra04286bopenalex-snapshot
Multicomponent gas separation and purification using advanced 2D carbonaceous nanomaterials
inferred← citeshttps://doi.org/10.1039/d1cp00207dopenalex-snapshot
Molecular dynamics simulations of simplified sodium borosilicate glasses: the effect of composition on structure and dynamics
inferred← citeshttps://doi.org/10.1039/d2me00041eopenalex-snapshot
An atomistic perspective on the diffusion and permeation of hydrogen and isotopes through an engineered nanoporous silica membrane using molecular dynamics simulations
inferred← citeshttps://doi.org/10.1039/d2me00094fopenalex-snapshot
BaO-doped silicate and borosilicate glasses for enhanced chemical durability: molecular dynamics simulations based strategy for glass design
inferred← citeshttps://doi.org/10.1039/d3cp02967kopenalex-snapshot
Enhancing the seawater desalination performance of multilayer reduced graphene oxide membranes by introducing in-plane nanopores: a molecular dynamics simulation study
inferred← citeshttps://doi.org/10.1039/d3me00118kopenalex-snapshot
Dehydration induced selective ion trapping by topology constrained atomically thin graphene-crown membranes
inferred← citeshttps://doi.org/10.1039/d3ra03867jopenalex-snapshot
Enhancing solubility and stability of sorafenib through cyclodextrin-based inclusion complexation: in silico and in vitro studies
inferred← citeshttps://doi.org/10.1039/d4su00251bopenalex-snapshot
Catalytic function of ionic liquids in polyethylene terephthalate glycolysis by molecular dynamics simulations
inferred← citeshttps://doi.org/10.1039/d4ta06413eopenalex-snapshot
Mechanisms of oxygen transport resistance of mesoporous carbon-supported catalysts in fuel cells
inferred← citeshttps://doi.org/10.1039/d5dd00508fopenalex-snapshot
DBMLFF: linear scaling machine learning force fields via electron density decomposition for molecular electrolytes
inferred← citeshttps://doi.org/10.1039/d6ra04601kopenalex-snapshot
Target deconvolution of a selective HepG2 cytotoxic hit identifies GSTP1 and TRAP1 as candidate molecular targets
inferred← citeshttps://doi.org/10.1039/d6ta04903fopenalex-snapshot
Fluorinated co-solvent drives anion-enriched solvation and NaF-rich cathode–electrolyte interphase for long-lifetime sodium-ion batteries
inferred← citeshttps://doi.org/10.1063/1.1324713openalex-snapshot
Optimal charge-shaping functions for the particle–particle—particle–mesh (P3M) method for computing electrostatic interactions in molecular simulations
inferred← citeshttps://doi.org/10.1063/1.1523915openalex-snapshot
Development of a simple, self-consistent polarizable model for liquid water
inferred← citeshttps://doi.org/10.1063/1.1574774openalex-snapshot
A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water
inferred← citeshttps://doi.org/10.1063/1.1624054openalex-snapshot
A fast-Fourier transform method to solve continuum-electrostatics problems with truncated electrostatic interactions: Algorithm and application to ionic solvation and ion–ion interaction
inferred← citeshttps://doi.org/10.1063/1.1747927openalex-snapshot
An application of flexible constraints in Monte Carlo simulations of the isobaric–isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model
inferred← citeshttps://doi.org/10.1063/1.1805516openalex-snapshot
Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice
inferred← citeshttps://doi.org/10.1063/1.1955525openalex-snapshot
Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations
inferred← citeshttps://doi.org/10.1063/1.2177249openalex-snapshot
Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: A continuum-electrostatics study
inferred← citeshttps://doi.org/10.1063/1.2201698openalex-snapshot
Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation
inferred← citeshttps://doi.org/10.1063/1.2206581openalex-snapshot
Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics
inferred← citeshttps://doi.org/10.1063/1.476022openalex-snapshot
Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural, and dielectric properties of liquid water
inferred← citeshttps://doi.org/10.1063/1.476320openalex-snapshot
Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential
inferred← citeshttps://doi.org/10.1063/1.477788openalex-snapshot
Ionic charging free energies: Spherical versus periodic boundary conditions
inferred← citeshttps://doi.org/10.1063/1.477873openalex-snapshot
Ewald artifacts in computer simulations of ionic solvation and ion–ion interaction: A continuum electrostatics study
inferred← citeshttps://doi.org/10.1063/1.479013openalex-snapshot
Polarization around an ion in a dielectric continuum with truncated electrostatic interactions
inferred← citeshttps://doi.org/10.1063/1.4896628openalex-snapshot
Real space electrostatics for multipoles. II. Comparisons with the Ewald sum
inferred← citeshttps://doi.org/10.1063/1.5007132openalex-snapshot
Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations
inferred← citeshttps://doi.org/10.1063/5.0107348openalex-snapshot
Rapid water dynamics structures the OH-stretching spectra of solitary water in ionic liquids and dipolar solvents
inferred← citeshttps://doi.org/10.1063/5.0302812openalex-snapshot
Performance comparison of slit and nanoporous graphene oxide membranes in water desalination
inferred← citeshttps://doi.org/10.1063/5.0321627openalex-snapshot
Thermodynamic discontinuity in evaporating thin solvated nematics
inferred← citeshttps://doi.org/10.1080/08927020701613623openalex-snapshot
Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability
inferred← citeshttps://doi.org/10.1080/08927020701783566openalex-snapshot
Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics
inferred← citeshttps://doi.org/10.1080/08927022.2014.913791openalex-snapshot
A determination of liquid–vapour interfacial properties for methanol using a linear-combination-based isotropic periodic sum
inferred← citeshttps://doi.org/10.1080/08927022.2014.998210openalex-snapshot
Application of isotropic periodic sum method for 4-pentyl-4′-cyanobiphenyl liquid crystal
inferred← citeshttps://doi.org/10.1080/08927022.2016.1271948openalex-snapshot
Combined use of periodic reaction field and coarse-grained molecular dynamics simulations. I. phospholipid monolayer systems
inferred← citeshttps://doi.org/10.1080/08927022.2017.1356458openalex-snapshot
Structural dynamics and binding free energy of neral-cyclodextrins inclusion complexes: molecular dynamics simulation
inferred← citeshttps://doi.org/10.1080/08927022.2023.2202764openalex-snapshot
Identification of novel potential hepatitis E virus inhibitors as seen from molecular docking, free energy landscape and molecular dynamics simulation studies
inferred← citeshttps://doi.org/10.1080/08927029808022044openalex-snapshot
An Iterative PPPM Method for Simulating Coulombic Systems on Distributed Memory Parallel Computers
inferred← citeshttps://doi.org/10.1088/1402-4896/ae5bd1openalex-snapshot
Molecular dynamics and time-frequency analysis of aqueous lubrication mechanisms at copper-polyethylene interfaces
inferred← citeshttps://doi.org/10.1088/1674-1056/ad57aeopenalex-snapshot
Theoretical insights into thermal transport and structural stability mechanisms of triaxial compressed methane hydrate
inferred← citeshttps://doi.org/10.1103/physreve.97.033306openalex-snapshot
Sensitivity of electrospray molecular dynamics simulations to long-range Coulomb interaction models
inferred← citeshttps://doi.org/10.1109/hpcc-smartcity-dss50907.2020.00014openalex-snapshot
Optimizing Astrophysical Simulation Software on Sunway Heterogeneous Manycore Architecture
inferred← citeshttps://doi.org/10.1109/tcad.2004.829798openalex-snapshot
A Parallel Fast Fourier Transform on Multipoles (FFTM) Algorithm for Electrostatics Analysis of Three-Dimensional Structures
inferred← citeshttps://doi.org/10.1110/ps.03137003openalex-snapshot
Molecular dynamics simulation of highly charged proteins: Comparison of the particle‐particle particle‐mesh and reaction field methods for the calculation of electrostatic interactions
inferred← citeshttps://doi.org/10.1142/s0217984905010207openalex-snapshot
A FAST BOUNDARY ELEMENT METHOD FOR UNDERWATER ACOUSTICS
inferred← citeshttps://doi.org/10.1146/annurev.pharmtox.37.1.71openalex-snapshot
STRUCTURE-BASED DRUG DESIGN:Computational Advances
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