T. E. Wainwright

Bio: T. E. Wainwright is an academic researcher. The author has contributed to research in topics: Motion (physics) & Equations of motion. The author has an hindex of 1, co-authored 1 publications receiving 2062 citations.

Phase Transition for a Hard Sphere System

Abstract: The method consists of solving exactly the simultaneous classical equation of motion of several hundred particles by means of fast electronic computers. (W.L.H.)

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Abstract: CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

CHARMM: the biomolecular simulation program.

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.

Gromacs 4.5

Abstract: Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. Availability: GROMACS is an open source and free software available from http://www.gromacs.org. Contact: erik.lindahl@scilifelab.se Supplementary information:Supplementary data are available at Bioinformatics online.

Statistical physics of social dynamics

Abstract: Statistical physics has proven to be a fruitful framework to describe phenomena outside the realm of traditional physics. Recent years have witnessed an attempt by physicists to study collective phenomena emerging from the interactions of individuals as elementary units in social structures. A wide list of topics are reviewed ranging from opinion and cultural and language dynamics to crowd behavior, hierarchy formation, human dynamics, and social spreading. The connections between these problems and other, more traditional, topics of statistical physics are highlighted. Comparison of model results with empirical data from social systems are also emphasized.

Studies in Molecular Dynamics. I. General Method

Abstract: A method is outlined by which it is possible to calculate exactly the behavior of several hundred interacting classical particles. The study of this many‐body problem is carried out by an electronic computer which solves numerically the simultaneous equations of motion. The limitations of this numerical scheme are enumerated and the important steps in making the program efficient on the computers are indicated. The applicability of this method to the solution of many problems in both equilibrium and nonequilibrium statistical mechanics is discussed.