Gabedit: the Portal to Chemistry
Many chemistry software applications are available for doing scientific work on Linux. I've covered several here in previous issues of the magazine, and of them have their own peculiar specialties—areas where one may work better than another. So, depending on what your research entails, you may need to use multiple software packages to handle all of the work. This is where Gabedit will step in to help you out.
Gabedit provides a single unified interface to a multitude of chemistry packages available on your system. It should be available within the package management systems for most distributions. For example, on Debian-based systems, you can install it with the command:
sudo apt-get install gabedit
Once it's installed, start it with the
gabedit command. The very first time you start Gabedit,
you'll see a series of windows describing all
the data directories that need to be created in order for Gabedit
to run. The pane on the left-hand side shows a listing of all the
chemistry programs you could use for your work. The central pane
provides two tabs, one for input and one for results.
Figure 1. When you first start Gabedit, you'll get an empty project where you can begin your work.
To start working with Gabedit, you need to create a new input file for the software package you want to work with. The icon bar across the top of the window provide buttons for the various types of input files that Gabedit can use. Clicking on one of them will pop up a new window where you can enter parameters relevant for that type of input file. For example, clicking on the first button pops up a window where you can create a new input file for GAMESS.
Figure 2. When you create a new input file, a new window pops up where you can enter the initial parameters.
If you try to do this at the beginning of your work, you'll actually get an error. All of these programs depend on some set of atoms, defined as a geometry, in order to do their calculations, which means you need to create this geometry first. Clicking the Geometry menu entry will provide a list of different options for creating a new geometry. The first two are specialized options for Gaussian and Molpro. For this example, let's use the two options at the bottom of the list. The first option pops up a new window where you can select the type of geometry (XYZ, for example) and then create a table of atoms used within your geometry.
Figure 3. You need to create a new geometry that will be used in the calculations.
Right-clicking inside the table of the geometry editor provides a pop-up menu where you can add a new entry to the table. This allows you to select the element, location and charge for the new point in the geometry. This geometry exists within the memory space of the current project, which means it will be available for other functions within Gabedit.
Figure 4. You can add individual elements, setting their chemical properties, to your geometry.
The other available geometry function is the draw function. You can access it via the Geometry→Draw menu item. This pops up a new window where you can visualize your molecule and manipulate it before doing any calculations.
Figure 5. You can use the draw functionality to visualize the geometry of your collection of atoms.
Here, you can edit the existing geometry and move elements around, or you can add or remove elements to the molecule. You even can add entire functional units, such as benzene rings or alcohol groups.
Once you have an input file, you need to run it through the appropriate software package in order to get results. If the programs you wish to use are installed on your local machine and are in your search path, it should just work out of the box. If they were installed in some other location, you need to tell Gabedit where they are. Clicking the Settings→Preferences menu item will bring up a new window where you can set the commands needed to run the relevant programs.
Figure 6. You can set the specific commands for each of the available chemistry packages.
You then can run the program either by clicking the run button in the icon bar or clicking the Run→Run a Computation Chemistry program menu item. This will present a new window where you can set the parameters for this run.
Figure 7. You can set the parameters for either a local run or a remote run within the same window.
For a local run, you can set parameters including which program to use, what folder to run in and the filenames and commands to execute. If you select "Remote host" instead, you can choose the protocol to communicate over and which host to communicate with. You also can set the user name and password to use, along with the working directory on the remote machine. If you find that your initial choice of program isn't optimal, you can try another. By clicking the Tools→Open Babel menu item, you get a window that allows you to do a translation of input file from one file format to another. This way, you can reuse your previous work within a different software package.
Gabedit is not only useful in setting up a computational chemistry problem and running it, but it's also useful in analyzing the results afterward. The analysis functions are available under the Tools menu item. You can select to load a file for a basic XY-plot, and you can select the Tools→XY plotter menu item to bring up the plot window. Right-clicking the plot window brings up a menu where you can change the options of the plot as well as load data files to be plotted. There also is an option to do contour plots by clicking the Tools→Contours plotter menu item.
Figure 8. You can do contour plots of the results from a computation.
Additionally, there is a whole series of spectrum analyses that you can apply as well. You can do IR, Rahman, UV and ECD spectral analysis. For each of these options in the Tools menu, you can load an output file from a number of different file formats, including a special Gabedit file format.
Under the NMR spectrum entry of the Tools menu, you can select to load either a previously calculated results file or the NMR Spin-Spin Splitting Simulation.
Figure 9. You can do NMR spectrum simulations for your molecule of choice.
Here you can set several options, such as the lineshape and the scaling. If you right-click the plot window, you have the same options as in the other plot windows. You also can add more data sets, change the plot details or the overall color theme.
With Gabedit, you can use quite a few of the available chemistry packages from a unified user interface. When doing more complicated research, or doing discovery work, being able to use multiple packages definitely will make everything easier to handle. You also can expand the options within Gabedit by adding your own functional units or altering the molecular mechanics parameters to be used in your work. Hopefully, Gabedit can help move your research into new areas.