An extension to the P(3)M algorithm for electrostatic interactions is presented that allows to efficiently compute dipolar interactions in periodic boundary conditions. Theoretical estimates for the root-mean-square error of the forces, torques, and the energy are derived. The applicability of the estimates is tested and confirmed in several numerical examples. A comparison of the computational performance of the new algorithm to a standard dipolar-Ewald summation methods shows a performance crossover from the Ewald method to the dipolar P(3)M method for as few as 300 dipolar particles. In larger systems, the new algorithm represents a substantial improvement in performance with respect to the dipolar standard Ewald method. Finally, a test comparing point-dipole-based and charged-pair based models shows that point-dipole-based models exhibit a better performance than charged-pair based models.
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http://dx.doi.org/10.1063/1.3000389 | DOI Listing |
Phys Chem Chem Phys
March 2022
Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
We investigate the translocation of rods with different charge distributions using hybrid Langevin dynamics and lattice Boltzmann (LD-LB) simulations. Electrostatic interactions are added to the system using the PM algorithm to model the electrohydrodynamic interactions (EHI). We first examine the free-solution electrophoretic properties of rods with various charge distributions.
View Article and Find Full Text PDFJ Comput Chem
July 2018
Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institue of Engineering Univ. Grenobl Alpes), LJK, Grenoble, 38000, France.
The computation of long-range potentials is one of the demanding tasks in Molecular Dynamics. During the last decades, an inventive panoply of methods was developed to reduce the CPU time of this task. In this work, we propose a fast method dedicated to the computation of the electrostatic potential in adaptively restrained systems.
View Article and Find Full Text PDFJ Phys Chem B
August 2016
Department of Physics, Shanghai Normal University, Shanghai 200234, China.
Continuum solvation modeling based upon the Poisson-Boltzmann equation (PBE) is widely used in structural and functional analysis of biomolecules. In this work, we propose a charge-central interpretation of the full nonlinear PBE electrostatic interactions. The validity of the charge-central view or simply charge view, as formulated as a vacuum Poisson equation with effective charges, was first demonstrated by reproducing both electrostatic potentials and energies from the original solvated full nonlinear PBE.
View Article and Find Full Text PDFJ Toxicol
August 2012
Département de Santé Environnementale et de Santé au Travail, Université de Montréal, Montreal, QC, Canada H3T 1A8.
The objective of this study was to evaluate the impact of whole- and sub-population-related variabilities on the determination of the human kinetic adjustment factor (HKAF) used in risk assessment of inhaled volatile organic chemicals (VOCs). Monte Carlo simulations were applied to a steady-state algorithm to generate population distributions for blood concentrations (CAss) and rates of metabolism (RAMs) for inhalation exposures to benzene (BZ) and 1,4-dioxane (1,4-D). The simulated population consisted of various proportions of adults, elderly, children, neonates and pregnant women as per the Canadian demography.
View Article and Find Full Text PDFJ Chem Phys
June 2010
Institut für Computerphysik, Universität Stuttgart, Pfaffenwaldring 27, 70569 Stuttgart, Germany.
The interlacing technique of Hockney and Eastwood is extended to the particle-particle, particle-mesh (P3M) algorithm with analytical and ik-differentiation that computes the approximate Coulomb forces between N point particles in a periodic box. Interlacing means that one makes two separate computations of the reciprocal-space Ewald force, using two grids shifted with respect to each other by half of the diagonal of the grid subcell, and then takes the average of the two forces. The resulting algorithms compare favorably against their own noninterlaced versions and against the interlaced smooth particle-mesh Ewald algorithm.
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