GridMol: Grid Application For Molecular Visualization And Modeling

With the development of computational chemistry and computer technology, many programs have been developed and applied for chemistry calculating, molecule visualization, molecule modeling, database searching and so on. Developing a platform integrating kinds of the programs to provide one-stop service has been becoming an important research field recently.Based on the idea of grid computing, we present GridMol, extensible implementation for model of the high performance computational chemistry platform. GridMol provides computational chemists one-stop service for molecule modeling, scientific computing and visualizing molecule. In term of molecule visualization, GridMol can be used to display three-dimension structure of many kinds of molecules in many modes, to examine the molecule parameters and to analyzing the calculation result. In the sense of molecule modeling, GridMol is used to modify molecular parameter and to add atom or radical for building new molecule. Because of the inappropriate structure of a newly built molecule, genetic algorithms and molecular mechanics are applied to optimize molecules. GridMol is also developed as an application of grid computing and now has been successfully deployed in China National Grid(CNGrid) and running as whole platform providing functions of molecular visualizing, molecular modeling and job submission.GridMol is coded using Java and Java3D for portability and cross-platform compatibility. Not only can it run as a stand-alone application, but also as an applet which can be accessed through web browsers. In this thesis, we will present the techniques for molecular visualization, molecular modeling, molecular structure optimization and job submission in grid computing. GridMol is available free of charge under the GNU Public License (GPL) from our website: http://www.sccas.cn/～syh/GridMol/index.html...