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MOPAC7 is a semi-empirical quantum-mechanics code written by James J. P. Stewart and co-workers. The purpose of this project is to maintain MOPAC7 as a stand-alone program as well as a library that provides the functionality of MOPAC7 to other programs.
Soft for ab initio and MD simulating of water system. Contains program for ICE: construct ice, specific monte-carlo simulation, proton rearrangement calculations; for PDB-water: calculate rotation energy profile, for Effective Fragment simulations.
A Molecular Chemical Viewer using OpenGL and Platform independent provided for the study of Chemicals, including physical, chemical and visual properties.
nmrproc shall be an NMR (nuclear magnetic resonance) data processing application supporting many file formats, a highly intuitive hence easy-to-use interface for routine NMR spectrum processing and generation of publication quality spectra.
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Mendeleev is a molecular weight calculator for PalmOS devices. Operation is simple -- just enter the formula for the molecule, and the molecular weight will be displayed.
OBExtensions is a extension library for the chemoinformatics library Openbabel.
It provides extensions to Openbabel, being mostly GUI widgets.
OBExtensions has a 2D/3D viewer, 2D coordinates generator and some other extensions.
Real-time volumetric rendering of four dimensional scientific data using OpenGL.Phaser is tool for drawing Ternary Phase diagrams.User can rotate,zoom,cut surface with different planes,compare different data sets and draw error bars for each point.
The ISOTOPIC PATTERN CALCULATOR is a small linux tool for mass spectrometry. It calculates the isotopic distribution for a given chemical formula or peptide sequence.
GIPS is a GUI Version of the Isotopic Pattern Calculator.
We use R (www.r-project.org) in order to generate a greater specificity and sensitivity of protein identification by Mass Spectrometry. These functions are implemented as add-on packages to the open source GPL software R.
runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.
qsims simulates quantum dynamics with an (almost) arbitrary time-dependent Hamiltonian. qsims uses a Chebychev polynomial expansion of the Schrodinger propagator, and the pseudospectral method developed by R. Kosloff.
Mole (Chemistry Calculator) can calculate molar mass, number of moles and atoms, empirical and molar formulas and can do stoichiometric calculations such as percent yield and limiting reactant. Mole can also do gas stoichiometry and gas law calculations.
The Synaptic Simulator is a program which simulates models of single neuronal synapses and compartments, complex constructs of such models. Furthermore the program is able to regain parameters by fitting simulated results with experimental data.
REMD toolkit is designed as a C++ framework to build a replica-exchange molecular dynamics (REMD) program, suitable for solving the multiple-minima problem that prevents accurate estimation of thermodynamical properties.
Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.
CHIMP aims to provide a complete suite of tools for the investigation and modeling of chemical systems. It currently is able to parse chemical reaction mechanisms and run kinetic Monte Carlo simulations on the reacting system.
GAST-Viz is a toolkit allowing for the creation of OpenGL atomistic simulation applications using discrete element modeling methods. A number of sample applications are included.