This is an implementation of the adaptive biasing force method (ABF) in NAMD. The code for ABF was developed by Eric Darve, Stanford University. ABF is a method created by E. Darve and A. Pohorille to calculate the free energy of bio-molecules.
Datagam is a tool for extracting data from output or punch files produced by GAMESS(US) or FireFly (old name PC GAMESS) packages. Mac GUI wrapper also available.
Upstream version of the project goes to the launchpad. Only final versions of the sourcecode and compiled binars will be available from this domain.
Goal: to make a lean, mean C++ engine capable of handling complex mathematical computations and to create a separate MFC (native C++) UI. NB: Project has been moved to Google Code: http://code.google.com/p/ultimath/
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ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.
ChemHelper is aimed at high school students and anybody that does not have a good understanding of chemistry. The objective is to have a program that can teach the basics of chemistry, by having interactive tutorials.
PIMC++ is a code designed to perform fully-correlated simulations of quantum systems in continuous space at finite temperature using Path Integral Monte Carlo.
It is designed in a modular way to facilitate easy addition of new algorithms.
Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Sourcecode is contained in jar files. Download contains GSH reactivity plugin.
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ReactionLab is a software package aimed for a unified computer environment to kinetic modeling of chemical reaction systems. The present implementation is founded on Matlab and Java-Swing GUI, with an interface to legacy C (and Fortran) codes.
Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.
The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and sourcecode repository can be found on https://jchempaint.github.io
dmcut2 is a scientific program designed to simulate chemical reactions at surfaces using Metropolis and Monte-Carlo methods. Short ranged interactions between adsorbates may be taken into account. Emphasis was put on code readability and usability.