Running A + BC ==> AB + C
In order to run the reaction you need to start the program and choose the reaction A + BC ==> AB + C
 Hit return when you see this screen
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 Click on the A + BC ==> AB + C button and hit return when you see this screen
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Click here for detailed instructions for these startup screens
Next you are presented with a dialog which looks like:
For more information about these cases click here
Go dialog
Next machine makes many plots. The plots will be described below. Eventually you are presented with a button labeled "click here to start the trajectories"
You must hit enter or push the button to go on!
Running The Program
Next you get a very complicated looking screen: There are four windows to display the trajectories and many buttons

Let us go through the parts of the screen. First let us consider the various windows. There are four windows labeled "Plot on potential energy surface", "Plot on mass weighted potential energy surface", "animation", "Positions vs time". You can click on each window to bring it forward and watch the plots. Then there are some controls along the top of the screen. We will discuss each part below.
General controls
The Image below shows the general controls

You do not need to use any of the controls to run the program. However, if you click on the buttons you can change how the program performs.
- File, and Edit are commands which work best after the program has stopped.
- Edit lets you select parts of the screen for printing
- File lets you save that part to a file or print it
- View lets you change the size of the window.
- State lets you pause execution of the program for printing or to resume printing
- Window lets you cascade or tile the various plots.
- Tile the plots and move the sliders if you want to see all four plots at once
- Help gives help screens
- Xcelerate lets you speed up the trajectories
- Slow Down lets you slow down the trajectories
- Stop and restart lets you stop execution and either start over or exit
- If you choose exit, you will not actually exit until you close all windows. (That lets you print screens after execution). If you want to exit completely type alt-f4
- Display run parameter gives you a plot out of all of the run parameters. Click here to see what all of the parameters mean.
- You can also close the program or any of the individual plots using the boxes on the right of the screen.
Next it is useful to discuss the plots
Plot on potential energy surface
The first plot is a plot a potential energy surface. Here is a picture of the potential energy surface.
The potential energy surface is a contour plot of the potential energy of the system as a function of r_AB the distance from A to B and r_BC the distance from B to C. The Y axis in the plot is the distance from A to B. The X axis in the plot is the distance from B to C. The reactants are in the upper left of the contour plot; the products are in the lower right of the contour plot. There are contours for E= 9, 15, and 24 kcal/mole. The saddle point is indicated by the red dot. There is also a 45 degree line so you can see whether you have an early or late transition state.
Students sometimes have trouble seeing contour plots of potential energy surfaces. There is a tutorial on contour plots in examples 7G and 8A of R. I. Masel, Kinetics and Catalysis, Wiley 2001. There is also an excel spreadsheet which displays contour plots and allows students to manipulate them. The spreadsheet is available from The wiley website
Trajectories on potential energy surfaces
Here are two trajectories on a potential energy surface.
The trajectories are plots of the A-B and B-C distances versus time when the reactants collide. The black trajectory connects reactants to products so it is a reactive trajectory. The green trajectory goes from the reactants to the transition state and back to the reactants so it is an unreactive trajectory.
There is some other information on the plots of the energy versus time. The additional information includes the date and time in the format day/month/year, the saddle point energy and the collisional energy (i.e. the sum of the kinetic and potential energy for the reactants).
Plot on a mass weighted potential energy surface

There is a subtlety in trajectories on standard potential energy surfaces in that there is some curvature in the trajectories since newton's equation of motion do not separate in r_ab and r_bc coordinates. People use mass weighted coordinates, or the affine transformation to avoid this error. There is a description of the affine transformation in section 8.16 of R. I. Masel, Kinetics and Catalysis, Wiley 2001. We plot the trajectory on mass weighted coordinates in the second window. Once the program is running, you can click anywhere on the window to bring the plot forward.
Animation
We also include an animation of the reaction to help students see the motion. Once the program is running, you can click anywhere on the window to bring the animation forward. Then you can watch the positions of the atoms evolve. Look at the final state. A comes in. Does A scatter away or does C fly away? When does it happen? All of these questions can be answered by looking at the animations.
Positions versus time

Finally we include a plot of the position versus time. Once the program is running, you can click anywhere on the window to bring the animation forward. The plot shows the bond lengths versus time. In the green trajectory, A comes in B and C and eventually C flies away. A discussion of these plots can be found in Chapter 8 of R. I. Masel, Kinetics and Catalysis, Wiley 2001
The ending dialog
After all of the trajectories run you will be presented with a dialog like:

- Hit the top button if you want to see the same cases again.
Note 1) the system picks random initial positions for the trajectories so if you run a second time the results will be slightly different.
2) The machine does not reset the speed when you hit this button. Please hit the "Continue: Use Different Parameters" button to reset the speed.
- Hit the second button to continue running the program with different parameters
Also use this button if you want to reset the plotting speed to it's original value.
- Hit the third button to print the screens.
Note the program actually creates an image of the screens on disk and then prints the image. That works fine with windows 95/98/ME. The print statement might or might not work with correctly Windows NT/2000. (The program needs to have permission to write to the disk for the printing to work correctly from NT). If the printing does not work correctly, you can still print by hitting the exit button, but choose to not close the windows (see below). You can then print each window by clicking on the window, clicking on the edit menu and selecting all, then clicking on the file menu and selecting print.
- Hit the bottom button to exit
- Note: the program does not actually exit when you hit the exit button. Instead it gives you a dialog:

Hit yes if you want to exit the program. Hit no if you want to keep the windows open for printing. You can then print each window by clicking on the window, clicking on the edit menu and selecting all, then clicking on the file menu and selecting print.
Hit alt-f4 to exit after you are done printing.
There is more information on the ReactMD website.
Click here to visit the ReactMD website
Click here for updates to the documentation
For further information about applications of this program please look in
Chapter 9 of R. I. Masel, Principles of Adsorption and Reaction on Solid Surfaces, Wiley 1996 or
Chapter 8 of R. I. Masel, Kinetics and Catalysis, Wiley 2001