Author

# S. W. de Leeuw

Bio: S. W. de Leeuw is an academic researcher from Odense University. The author has contributed to research in topics: Periodic boundary conditions & Dielectric. The author has an hindex of 2, co-authored 2 publications receiving 1245 citations.

##### Papers

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TL;DR: In this paper, the effective interactions of ions, dipoles and higher-order multipoles under periodic boundary conditions are calculated where the array of periodic replications forms an infinite sphere surrounded by a vacuum.

Abstract: The effective interactions of ions, dipoles and higher-order multipoles under periodic boundary conditions are calculated where the array of periodic replications forms an infinite sphere surrounded by a vacuum. Discrepancies between the results of different methods of calculation are resolved and some shape-dependent effects are discussed briefly. In a simulation under these periodic boundary conditions, the net Hamiltonian contains a positive term proportional to the square of the net dipole moment of the configuration. Surrounding the infinite sphere by a continuum of dielectric constant e.9 changes this positive term, the coefficient being zero as e9 ->∞ . We report on the simulation of a dense fluid of hard spheres with embedded point dipoles; simulations are made for different values of showing how the Kirkwood gr-factor and the long-range part of hA (r) depend on e9 in a finite simulation. We show how this dependence on e9 nonetheless leads to a dielectric constant for the system that is independent of e . In particular, the Clausius-Mosotti and Kirkwood formulae for the dielectric constant e of the system give consistent e values.

1,060 citations

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TL;DR: In this article, a perturbation theory expressing correlation functions with e" in terms of correlation function with e9 exactly to order N* 1, N being the number of particles in the sample.

Abstract: We consider simulations of dipolar systems under periodic boundary conditions in which a large sphere consisting of periodic replications of a central simulation cell is surrounded by a continuum of dielectric constant e9. We develop a perturbation theory expressing correlation functions with e" in terms of correlation functions with e9 exactly to order N* 1 , N being the number of particles in the sample. In the thermodynamic limit, the correlation functions and internal energy density are independent of e The Kirkwood g -factor is strongly dependent on e 9 but in such a way as to make the dielectric constant independent of e9. The dependence upon e9 of h A {r) at large r, described in paper I, is explained in terms of the perturbation series.

185 citations

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TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.

Abstract: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.

20,639 citations

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TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.

Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

15,288 citations

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TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.

Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

13,210 citations

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TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.

Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

5,997 citations

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TL;DR: The General Utility Lattice Program (GULP) as discussed by the authors has been extended to include the ability to simulate polymers and surfaces, as well as adding many other new features, and the current status of the program is fully documented.

Abstract: The General Utility Lattice Program (GULP) has been extended to include the ability to simulate polymers and surfaces, as well as adding many other new features, and the current status of the program is fully documented. Both the background theory is described, as well as providing a concise review of some of the previous applications in order to demonstrate the range of its use. Examples are presented of work performed using the new compatibilities of the software, including the calculation of Born effective charges, mechanical properties as a function of applied pressure, calculation of frequency-dependent dielectric data, surface reconstructions of calcite and the performance of a linear-scaling algorithm for bond-order potentials.

1,793 citations