Showing papers in "Computer Physics Communications in 1995"

TL;DR: A parallel message-passing implementation of a molecular dynamics program that is useful for bio(macro)molecules in aqueous environment is described and can handle rectangular periodic boundary conditions with temperature and pressure scaling.

TL;DR: The development, current features, and some directions for future development of the AMBER package of computer programs are described, embodying a number of the powerful tools of modern computational chemistry-molecular dynamics and free energy calculations.

TL;DR: In this article, the problem of unbiasing and combining the results of umbrella sampling calculations is reviewed, and the weighted histogram analysis method (WHAM) of S. Kumar et al. is described and compared with other approaches.

TL;DR: A general-purpose Brownian dynamics program that has been developed at the University of Houston is described in this paper, where the diffusion of flexible chains is modeled by the finite difference solutions of the linearized Poisson-Boltzmann equation.

TL;DR: In this article, a Monte Carlo collision (MCC) package including the null collision method has been developed, as an addition to the usual PIC charged particle scheme which will be discussed here.

TL;DR: In this article, an extension to solid mechanics of the FLIP particle-in-cell method is presented, which uses two representations of the continuum, one based on a collection of material points and the other based on computational grid.

TL;DR: RMATRX1 as mentioned in this paper is a general program to calculate atomic continuum processes using the R -matrix method, including electronatom and electron-ion scattering, and radiative processes such as bound-bound transitions, photoionization and polarizabilities.

TL;DR: The resulting code architecture, OOPIC (object-oriented particle-in-cell), is a two-dimensional relativistic electromagnetic PIC code that encapsulates key PIC algorithms and data into objects, simplifying extensions such as new boundary conditions and field algorithms.

TL;DR: In this article, a comparison between comprehensive linear gyrokinetic calculations employing the ballooning formalism for high-n (toroidal mode number) toroidal instabilities are described.

TL;DR: MAGIC is a user-configurable code that solves Maxwell's equations together with Lorentz particle motion and a programmable processor named POSTER provides advanced post-analysis of the field and particle solutions.

TL;DR: In this article, the complete set of energy parameters used in the ENCAD (Energy Calculation and Dynamics) simulation program is presented, including the form of the potential, which has been designed for efficient simulation of trajectories of macromolecules in solution.

TL;DR: In this paper, the two phase flow of a dusty gas using SPH is formulated and extended to deal with gas, solid and liquid phases in each of which there may be several species.

TL;DR: In this article, a version of the smooth particle hydrodynamics (SPH) method suitable for modeling solids is described, which includes strength and implements a von Mises yielding relation for stresses beyond the Hugoniot elastic limit.

TL;DR: RAPGAP as mentioned in this paper generates ep collisions where the electron is scattered on a pomeron P coupled to the proton p. A gap in rapidity between the fast moving proton and the remaining hadronic system is observed.

TL;DR: In this paper, a transfer matrix technique is used to calculate the photonic band structure and transmission and reflection coefficients of photons incident on a complex metallic or dielectric structure, and the method is sufficiently general that any system with a well-defined unit cell can be studied.

TL;DR: In this article, a Monte Carlo program is presented that computes all four-fermion processes in e+e− annihilation, and a systematic, modular and self-optimizing strategy is adopted for the Monte Carlo integration, which serves also as an example for further event generators in high energy particle physics.

TL;DR: In this article, a hybrid scheme for cosmological simulations that incorporates a Lagrangean particle-mesh (PM) algorithm to follow the collisionless matter with the higher order accurate piecewise parabolic method (PPM) to solve the equations of gas dynamics is described.

TL;DR: This work describes the implementation of the parallel hashed oct-tree (HOT) code, and in particular its application to neighbor finding in a smoothed particle hydrodynamics (SPH) code.

TL;DR: In this paper, the JUMNA program for the energy optimisation of nucleic acids and nucleic acid-ligand complexes is described, including the force field used, input and output data, various options for symmetry, conformational constraints and energy mapping as well as recent combinatorial search techniques.

TL;DR: In this paper, the authors describe a method of characteristics-constrained transport (MCT) scheme that uses information propagated along Alfven characteristics to compute electromagnetic forces at intermediate time levels for the induction equation and for the Lorentz force.

TL;DR: In this article, the authors discuss two ways in which parton shower algorithms can be supplemented by matrix-element corrections to ensure the correct hard limit: by using complementary phase-space regions, or by modifying the shower itself.

TL;DR: The Monte Carlo integration and event generation package BASES/SPRING, upgraded so as to generate events with 50 independent variables, and to integrate functions with an alternating sign, is found to be useful in the numerical evaluation of interference effects among various amplitudes.

TL;DR: In this paper, a FORTRAN 77 subroutine package for the numerical solution of the Schrodinger and Dirac wave equations for central fields is presented, such that the function ν ( r ) ≡ rV( r ) is finite for all r and tends to constant values for r → 0 and r → ∞.

TL;DR: A package of computer programs for molecular dynamics simulations-MOIL-is described, which enables the study of macromolecules with potentials consistent with the AMBER/OPLS force field.

TL;DR: In this paper, the authors present Monte Carlo methods with a correct real-time dependence for simulating chemical reactions on a surface that have reaction-rate constants that may vary in time.

TL;DR: In this paper, a new package for solving the external region scattering problem is described, which uses a combination of R-matrix propagation techniques to ensure optimum stability and efficiency in integrating the coupled Schrodinger equations, and the radial distance over which the equations must be integrated is minimized by matching to an asymptotic wave function determined by an accelerated Gailitis expansion.

TL;DR: In this paper, a new pressure coupling method is described that combines Monte Carlo volume-space sampling with traditional molecular dynamics calculations to simulate the physical properties of molecular systems under standard conditions, where the pressure is maintained by accepting or rejecting volume moves of newly propagated configurations using the Metropolis algorithm with probability P(ΔV) = min (1, exp (( −1 kT 0 ){ΔE + P 0 ΔV − NkT 0 ln [ (V + ΔV) V ]})).

TL;DR: The DVR3D program suite as mentioned in this paper calculates energy levels, wavefunctions, and where appropriate dipole transition moments, for rotating and vibrating triatomic molecules using a Discrete Variable Representation (DVR).

TL;DR: An efficient algorithm for solving Poisson's equation in two and three spatial dimensions is discussed in this paper, where spherical coordinates and an expansion into spherical harmonics are used to solve the problem.

TL;DR: nMOLDYN as mentioned in this paper is a modular program package for the analysis of molecular dynamics simulations, especially designed for the computation and decomposition of neutron scattering spectra, which can be characterized in terms of various space and time correlation functions.