Molecular Modeling

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. This project offers a flexible rendering engine and a powerful plugin architecture. The main concept behind Avogadro... Platforms: *nix

BALLView is our standalone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality. It is available free of charge under the GPL for Linux, Windows and MacOS. It provides fast OpenGL-based visualization of... Platforms: Windows

A Java based molecular modeling program. Has support for generating movies by interpolating between given positions, interactive display and manipulation of atoms and bonds, and dynamic modeling of substance formation. Platforms: Windows, Mac, Linux

The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in computational structural biology to facilitate and standardize the development of molecular modeling, design and analysis tools. Platforms: *nix

Biomolecule Toolkit project is an Open Source library for the structural modeling of biological macromolecules. The toolkit provides a C++ interface for common tasks in computational structural biology, to facilitate the development of molecular modeling, design, and analysis tools. Whats New... Platforms: *nix

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded... Platforms: Mac, Linux

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Platforms: *nix

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. * Ready-to-use... Platforms: Windows, Mac, *nix, C/C++, BSD

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Cross-Platform: Molecular... Platforms: *nix

The EJS Molecular Dynamics Demonstration model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated Time step. For sufficiently small... Platforms: Mac

The EJS Molecular Dynamics model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated time step. For sufficiently small time steps dt,... Platforms: Mac

The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for an article by Eric Gislason "A close examination of the motion of an adiabatic piston" in the... Platforms: Mac

If you have read about direct modeling, you know it is the best approach for rapid creating flexible 3D designs. Now, PTC brings you a free download from the Creo product family - Creo Elements/Direct Modeling Express 4.0, a 3D CAD system you can use to create assemblies with up to 60 parts. *... Platforms: Windows

The APMonitor Modeling Language is optimization software for differential and algebraic equations. It is coupled with large-scale nonlinear programming solvers for data reconciliation, real-time optimization, dynamic simulation, and nonlinear predictive control. It is available as a free web... Platforms: Windows

The Java Modeling Language (JML) is a behavioral interface specification language that can be used to specify the behavior of Java modules. It combines the design by contract approach of Eiffel and the model-based specification approach of the Larch family of interface specification languages,... Platforms: Windows, Mac, *nix, Java, BSD Solaris

Hidden Markov models are used to describe the "stepping" behavior of molecular motors, as measured by single-molecule fluorescence techniques. Our HMM implementation is more versatile than the one described by Milescu, et al. Biophys. J. 91:3135-3150 and can be used as a "blind" step detector or... Platforms: Matlab

This ZIP-file contains the demonstration files used during the "Analog and Mixed-Signal Circuit Modeling with Simulink Product Family" webinar presented on June 22, 2004. Platforms: Matlab

Companion Software for the Dynamic Modeling and Control of Engineering Systems, 2e book by J. Lowen Shearer, Bohdan T. Kulakowski & John F. Gardner Platforms: Matlab

HOT is a package originally constructed for combustion modeling in Matlab. It calculates common thermodynamic properties such as enthalpy, specific heat, entropy, internal energy, gamma, ideal gas constant, molecular weight, etc Platforms: Matlab

Highlights include:d-deD? Integrating data sourcesd-deD? Valuing and creating a variable annuity productd-deD? Application development and deploymentThis webinar is relevant to practitioners or academics in finance whose focus is quantitative analysis, modeling, risk analysis, and... Platforms: Matlab