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Sidler D, Frasch S, Cristòfol-Clough M, Riniker S. Anisotropic reaction field correction for long-range electrostatic interactions in molecular dynamics simulations. J Chem Phys 2018; 148:234105. [PMID: 29935522 DOI: 10.1063/1.5007132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Reaction-field (RF) methods have been extensively used in molecular dynamics simulations to efficiently compute long-range electrostatic interactions. They assume a continuous dielectric medium outside a certain cutoff, which has shown to be a reasonable approximation in many cases. However, lattice sum or fast multipole methods are nowadays often used instead, which treat long-range interactions explicitly but may introduce different artefacts. In the following work, the major issue of RFs is addressed, i.e., their inability to account for inhomogeneity even in heterogenous environments (e.g., membranes or protein binding pockets). By using a first-order Laplace series expansion of the dielectric permittivity on the cutoff sphere, local anisotropic effects can be described in a simple form. It is shown that the resulting boundary-value problem cannot be solved analytically, but instead a well-behaved approximative anisotropic reaction field (ARF) is introduced, which preserves coordinate invariance and approaches the standard RF solution for homogeneous systems. The comparison of RF to the state-of-the-art particle-particle particle-mesh (P3M) method shows a difference in the orientation of molecules close to the interface between two different dielectrics (water/chloroform). It was found that the ARF leads to a correction of the orientational distribution toward the P3M reference for planar and spherical interfaces.
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Affiliation(s)
- Dominik Sidler
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Simon Frasch
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | | | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Toivanen EA, Losilla SA, Sundholm D. The grid-based fast multipole method – a massively parallel numerical scheme for calculating two-electron interaction energies. Phys Chem Chem Phys 2015; 17:31480-90. [DOI: 10.1039/c5cp01173f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A grid-based fast multipole method has been developed for calculating two-electron interaction energies for non-overlapping charge densities.
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Affiliation(s)
| | | | - Dage Sundholm
- Department of Chemistry
- University of Helsinki
- Finland
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3
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Arnold A, Fahrenberger F, Holm C, Lenz O, Bolten M, Dachsel H, Halver R, Kabadshow I, Gähler F, Heber F, Iseringhausen J, Hofmann M, Pippig M, Potts D, Sutmann G. Comparison of scalable fast methods for long-range interactions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:063308. [PMID: 24483585 DOI: 10.1103/physreve.88.063308] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Indexed: 06/03/2023]
Abstract
Based on a parallel scalable library for Coulomb interactions in particle systems, a comparison between the fast multipole method (FMM), multigrid-based methods, fast Fourier transform (FFT)-based methods, and a Maxwell solver is provided for the case of three-dimensional periodic boundary conditions. These methods are directly compared with respect to complexity, scalability, performance, and accuracy. To ensure comparable conditions for all methods and to cover typical applications, we tested all methods on the same set of computers using identical benchmark systems. Our findings suggest that, depending on system size and desired accuracy, the FMM- and FFT-based methods are most efficient in performance and stability.
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Affiliation(s)
- Axel Arnold
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Florian Fahrenberger
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Olaf Lenz
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
| | - Matthias Bolten
- Department of Mathematics and Science, University of Wuppertal, Wuppertal, Germany
| | - Holger Dachsel
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Rene Halver
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ivo Kabadshow
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Franz Gähler
- Faculty of Mathematics, Bielefeld University, Bielefeld, Germany
| | - Frederik Heber
- Institute for Numerical Simulation, University of Bonn, Bonn, Germany
| | | | - Michael Hofmann
- Department of Computer Science, Chemnitz University of Technology, Chemnitz, Germany
| | - Michael Pippig
- Department of Mathematics, Chemnitz University of Technology, Chemnitz, Germany
| | - Daniel Potts
- Department of Mathematics, Chemnitz University of Technology, Chemnitz, Germany
| | - Godehard Sutmann
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany and ICAMS, Ruhr-University, Bochum, Germany
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4
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García-Risueño P, Alberdi-Rodriguez J, Oliveira MJT, Andrade X, Pippig M, Muguerza J, Arruabarrena A, Rubio A. A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations. J Comput Chem 2013; 35:427-44. [DOI: 10.1002/jcc.23487] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 10/13/2013] [Accepted: 10/13/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Pablo García-Risueño
- Institut für Physik; Humboldt Universität zu Berlin; Zum grossen Windkanal 6 12489 Berlin Germany
- Institute for Biocomputation and Physics of Complex Systems BIFI; Universidad de Zaragoza C/ Mariano Esquillor; 50018 Zaragoza Spain
- Instituto de Química Física Rocasolano (CSIC); C/ Serrano 119 28006 Madrid Spain
| | - Joseba Alberdi-Rodriguez
- Department of Computer Architecture and Technology; University of the Basque Country UPV/EHU; M. Lardizabal, 1 20018 Donostia/San Sebastián Spain
- Nano-Bio Spectroscopy Group and European Theoretical Spectroscopy Facility; Spanish node; University of the Basque Country UPV/EHU; Edif. Joxe Mari Korta, Av. Tolosa 72 20018 Donostia/San Sebastián Spain
| | - Micael J. T. Oliveira
- Center for Computational Physics; University of Coimbra; Rua Larga 3004-516 Coimbra Portugal
| | - Xavier Andrade
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford Street Cambridge Massachusetts 02138
| | - Michael Pippig
- Department of Mathematics; Technische Universität Chemnitz; 09107 Chemnitz Germany
| | - Javier Muguerza
- Department of Computer Architecture and Technology; University of the Basque Country UPV/EHU; M. Lardizabal, 1 20018 Donostia/San Sebastián Spain
| | - Agustin Arruabarrena
- Department of Computer Architecture and Technology; University of the Basque Country UPV/EHU; M. Lardizabal, 1 20018 Donostia/San Sebastián Spain
| | - Angel Rubio
- Nano-Bio Spectroscopy Group and European Theoretical Spectroscopy Facility; Spanish node; University of the Basque Country UPV/EHU; Edif. Joxe Mari Korta, Av. Tolosa 72 20018 Donostia/San Sebastián Spain
- Centro de Física de Materiales, CSIC-UPV/EHU-MPC and DIPC; 20018 Donostia/San Sebastián Spain
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Bannasch G, Killian TC, Pohl T. Strongly coupled plasmas via Rydberg blockade of cold atoms. PHYSICAL REVIEW LETTERS 2013; 110:253003. [PMID: 23829735 DOI: 10.1103/physrevlett.110.253003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Indexed: 06/02/2023]
Abstract
We propose and analyze a new scheme to produce ultracold neutral plasmas deep in the strongly coupled regime. The method exploits the interaction blockade between cold atoms excited to high-lying Rydberg states and therefore does not require substantial extensions of current ultracold plasma experiments. Extensive simulations reveal a universal behavior of the resulting Coulomb coupling parameter, providing a direct connection between the physics of strongly correlated Rydberg gases and ultracold plasmas. The approach is shown to reduce currently accessible temperatures by more than an order of magnitude, which opens up a new regime for ultracold plasma research and cold ion-beam applications with readily available experimental techniques.
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Affiliation(s)
- G Bannasch
- Max Planck Institute for the Physics of Complex Systems, D-01187 Dresden, Germany
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