Molecular dynamics computations make up a very large proportion of the computer cycles being used in science today. For those of you who remember chemistry and or thermodynamics, you should recall that all of the calculations you made were based on treating the material in question as a homogeneous mass where each part of the mass simply has the average value of the relevant properties.

Many programs exist that try to serve as a replacement for MATLAB. They all differ in their capabilities—some extending beyond what is available in MATLAB, and others giving subsets of functions that focus on some problem area. In this article, let's look at another available option: FreeMat.

I've already looked at some GIS applications available on Linux. Programs like GRASS and qgis provide a full set of tools to do GIS. Sometimes, that's really overkill though. You may just want to display some data geographically and create a map. For those cases, there is Thuban, an interactive geographic data viewer.

Because the August issue's theme is programming, I thought I should cover some of the more-advanced features available in OpenMP.

In many cases, scientific research takes you into totally new areas of knowledge, never before explored by others. This means the computational work you need to do may be totally new as well. Although typically such code development still happens in C or FORTRAN, Python is growing in popularity. This is especially true in physics.

My last several articles have covered lots of software for doing research in the sciences. But one important area I haven't covered in detail is the resources available for teaching the next generation of computational scientists. To fill this gap, you can use the code provided through the Open Source Physics project.

A lot of the software packages I've covered in recent articles have been focused strictly on doing computations on your machine, separate from the real world. So in this article, I explore how to use your computer to design something you can build and use in the real world: your own model rocket.

In these columns, I have covered several different scientific packages for doing calculations in many different areas of research. I also have looked at various packages that handle graphical representation of these calculations. But, one package that I've never looked at before is gnuplot (http://www.gnuplot.info).

Many of my previous articles have looked at software packages that do scientific calculations and generate scientific results. But, columns of numbers are nearly impossible to make sense of—at least, by regular human beings. So what can you do? The answer is visualization.

In quantum physics, one of the calculations you might want to do is figure out how two or more particles may interact. This can become rather complicated and confusing once you get to more than two particles interacting, however. Also, depending on the interaction, there may be the creation and annihilation of virtual particles as part of the interaction.

One area of physics that is hard to wrap your head around is relativity. Basically, relativity breaks down into general and special relativity. General relativity deals with large masses and high energies, and it describes how space-time is warped by these. Special relativity deals with what happens during high velocities.

NASA has started a rather ambitious project: to provide open-source everything. The main site is located at http://open.nasa.gov. From here, there is access to data, code and applications, among other things. This is a great launching point for anyone interested in space science and NASA work.

In this article, I'm diving into chemistry again. Many packages, both commercial and open source, are available to make chemistry calculations at the quantum level. The one I cover here is gromacs (http://www.gromacs.org). It should be available for your distribution via its package manager.

I've realized I've missed out on a huge area of computational science—chemistry. Many packages exist for doing chemistry on your desktop. This article looks at a general tool called avogadro. It can do computations of energy and gradient values. Additionally, it can do analysis of molecular systems, interface to GAMESS and import and export from and to several file formats.