OpenScience / Software / Chemistry



Protomol

Posted on February 18, 2005 by Dan Gezelter

ProtoMol is a high-performance framework in c++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates … Continue reading →

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Posted in Theoretical and Computational | Leave a comment

LAMMPS

Posted on January 12, 2005 by Dan Gezelter

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, or granular systems using a variety of force fields and boundary conditions. Find … Continue reading →

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Posted in Molecular Dynamics | Leave a comment

Gabedit

Posted on October 5, 2004 by Dan Gezelter

Gabedit is a graphical interface to Gaussian, Molcas and Molpro computational chemistry packages running locally or on a remote server. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported and graphics can be exported … Continue reading →

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Posted in Chemistry | Leave a comment

GXSM

Posted on September 22, 2004 by Dan Gezelter

The Gnome X Scanning Microscopy project is a powerful graphical interface for any kind of 2D and 3D (multilayered 2D mode) data acquisition methods, especially designed for SPM and SPA-LEED, which are used in surface science. It includes methods for … Continue reading →

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Posted in Surfaces | Leave a comment

GAMGI

Posted on September 21, 2004 by Dan Gezelter

The General Atomistic Modelling Graphic Interface. GAMGI aims to be useful for: 1) the scientific community working in Atomistic Modelling, that needs a graphic interface to build input data and to view and analyse output data, calculated with Ab-Initio and … Continue reading →

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Posted in Molecule Viewers and Editors | Leave a comment

MCCCS Towhee

Posted on August 18, 2004 by Dan Gezelter

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been … Continue reading →

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Posted in Monte Carlo methods | Leave a comment

OOPSE

Posted on August 9, 2004 by Dan Gezelter

OOPSE is a new molecular dynamics simulation program which is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded … Continue reading →

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Posted in Molecular Dynamics | Leave a comment

The Molecular Workbench Software

Posted on July 14, 2004 by Dan Gezelter

The Molecular Workbench is a set of tools that can be used to compute and visualize the motion of ensembles of atoms and molecules. The motion of each entity is estimated using classical dynamics and applicable forces, including van der … Continue reading →

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Posted in Molecular Dynamics | Leave a comment

EChem++

Posted on June 18, 2004 by Dan Gezelter

a problem solving environment (PSE) for electrochemical experiments. This PSE is intended to provide support for the definition of electrochemical experiments, their control, simulation, and analysis. Find EChem++ at: http://www.echem.uni-tuebingen.de/~bs/echem/software/EChem++/echem++.shtml

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Posted in Electrochemistry | Leave a comment

PerlMol — Perl Modules for Molecular Chemistry

Posted on April 23, 2004 by Dan Gezelter

PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging". Find PerlMol — … Continue reading →

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Posted in Chemistry | Leave a comment