You need to use the command prompt, dosbox, or dos itself to run it.
To start the command prompt, go to the Start menu, Programs, Accessories, and then Command Prompt.
In the command prompt, type:
c: (replace "c" with the drive letter which a-train is on)
cd\a-train (replace "a-train" with the name of the folder a-train is in)
atrain /480 /C /IBM
That should hopefully work. You could also create a shortcut for atrain.bat and put /480 /C /IBM after its target if you don't like typing every time you wish to start the game.
If you tried this before, I am sorry I misunderstood you. On the other hand, if you have never used the command prompt before, then you will have to learn to be able to change the settings on this game. You may want to read some dos tutorials for help.
Hope this helps.
k: