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Linux for Chemists Linux is a great platform for working with science. There is an abundance of available
software that is useful to scientists, and a large support community on the internet.
The following programs are some of my choices for working with chemistry under Linux. Many of these applications are downloadable free of charge via the internet, which makes them especially attractive to students and researchers on a limited budget, or those who want to experiment risk free with something new. Molecule Viewing:JMol: free software written in Java, this program will display molecules from a number of imput formats, and can be used as an interface to PovRay for producing high quality ray traced images. JMol also animates vibrational modes of molecules, as output from Gaussian frequency calculations.Pymol: this free python program is my choice for generating simple animations of molecules as animated GIFs (like the rotating carborane cage below) and movies. The program features flexible molecule rendering (line, stick, ball, sphere, surfaces, etc.), and a built in ray tracing feature. 
Molecular Modeling:Gaussian: an extremely powerful commercial computational package. Not inexpensive, and the Linux version lacks a graphical frontend (WebMO, GaussView, and many other programs provide graphical access), but it is arguably the best and most comprehensive package available. Gaussian runs ab initio, semiempirical, and DFT calculations. It can be used for geometry optimization, calculation of vibrational frequencies, NMR shielding, thermochemistry, analysis of transition states, and much more.GAMESS: a free computational package. Like Gaussian, it lacks a graphical frontend, but its input and output are widely supported by other graphical programs. It is also useful for running ab initio and DFT calculations. Graphical Interfaces for Molecular Modeling Packages:WebMO: Available as both a free and commercial "Pro" version, WebMO is a very useful frontend for computational packages. The program provides a web interface, which can be accessed remotely by users through the internet, or locally. WebMO features a number of useful features, including job queuing and individual user account management. Tools for the creation or import of job input and analysis and export of job output are easy to use. WebMO is easy to install and upgrade, however, it requires a properly configured web server to be running as well.Manuscript Preparation:OpenOffice: OpenOffice is an office suite (similar to Microsoft Office) that features a word processor, spreadsheet, presentation program, and drawing program. The word processor has powerful built-in features for scientific writing, including a bibliographic database for storing and outputting references, and the ability to export documents in pdf format. The drawing program is excellent for editing graphical figures, especially where text labels and line art are needed. I used the OpenOffice suite to prepare my dissertation.My Dissertation - Juhasz.pdf (3.7 MB) GIMP: GNU Image Manipulation Program (GIMP), is a powerful graphics editor, with features and an interface similar to Adobe Photoshop. This is excellent for artistic edits of cover art and photographs. For example, I used GIMP to create the image below, which was published on the inside cover of Chemical Communications, Number 13, April 7, 2005.  Click to view the actual cover
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