Tinker with Molecular Dynamics for Fun and Profit

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All of these executables are designed to run as command-line programs. The output tends to be files of numbers, which are hard for a human to evaluate. The group who created TINKER also created a program called Force Field Explorer (FFE).

Figure 1. On initial startup, you will get an empty project window and a TINKER console.

The executables built above are not compiled to interface with FFE as is. If you want to compile your own copy and have it interact with FFE, it requires changing a number of source files. In this case, I would suggest that you go ahead and download one of the installation packages that include FFE. These come as a gzipped shell archive. After gunzipping it, you can run the shell script to start up the Java-based installer. It will let you select which portions to install along with FFE. Once it is all done, go ahead and start up FFE. It will open up the main window and a console window. From within FFE, you can load up structure files and start various TINKER analyses.

When you first open an .xyz file, the structure is rendered and displayed in the main window. You then can select the Modeling Commands tab to select which specific TINKER analysis to run. By default, these TINKER runs happen locally on the same machine, but it doesn't have to be this way. FFE gives you the option of connecting to a remote machine, likely more powerful than your desktop, and getting the actual TINKER programs to run over there.

Figure 2. You have access to all of the TINKER analysis routines, directly from FFE.

Once you have results, you can change the visual details like colors and whether to use wireframe or tube and so on. You also have the option of exporting a visual as an image file in one of several file formats.

I easily could fill the entire contents of Linux Journal just covering the most basic functionality TINKER provides. Hopefully, you will have seen enough to get an idea of whether this software might be of use to you. If so, a rather large amount of detailed documentation is available at the main TINKER Web site.

Resources

______________________

Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.

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