John W. Perram

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.

Abstract: Closed formulae for both real and reciprocal space parts of cutoff errors in the Ewald summation method in cubic periodic boundary conditions are derived. Such estimates are useful in tuning parameters in molecular simulations. Errors in both the electrostatic energy and forces are considered. The estimates apply to a disordered configuration of point charges and, with some limitations, also to point-charge molecular models. The accuracy of our estimates is tested and confirmed using simulated configurations of two systems (molten salt and diethylether) under a variety of conditions.

Abstract: Current supercomputers and the impending availability of large scale parallel machines makes possible the study by molecular dynamics of a number of fundamental problems in condensed matter science hitherto beyond our scope because of the enormous computing time involved. This is because a realistic model of such systems contains one or two orders of magnitude more particles than the systems studied to date. Moreover, the intermolecular forces between these particles will usually include contributions from distributions of permanent electric charges, so that the usual assumption of short-ranged forces cannot be made. We give a list of typical problems in this class and attack the problem of improving the performance of molecular dynamics algorithms to take advantage of these new architectures. We use the Jacobi theta function transformation to derive rapidly computable forms for the energy of and forces between large assemblies of N particles interacting in periodic boundary conditions as the sum of real ...

Abstract: In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath

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.

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

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.