First, download this file into your Gravity Simulator folder. Then use it instead of gravitysimulator.exe
http://orbitsimulator.com/gravity/beta/GravitySimulatorBeta2011May30.exe This is the beta version that lets you choose between Euler-Cromer and Runge Kutta 4. In the beta menu just choose which integrator you want.
If you want to edit it, you can either: 1) send me your changes and I'll do it for you, or 2) do it in C++, compile it into a dll named codepotomizer.dll, then replace the existing codeoptomizer.dll in your gravitysimulator folder, then finally, download the most recent beta version not counting 2011May30. Then it will use your C++ code instead.
To output data:
First, create a simulation and save it. It is recommended that you save it in its own folder.
File > Output File (don't choose systemic). Check the "Create Data File" box and the "Create Data File Copy" boxes. It then creates 2 files. The difference is that you can play around with the copy while the simulation is running. For example, if you open the data file in Excel, then Gravity Simulator can not write to the file. The original copy cares about this, while the copy does not. The copy won't update again until you close it in Excel, then it will copy the original version so they're identical again. Then choose how often you want the data to be written to the files, and the maximum number of data samples. Then choose for which objects, and finally choose what orbital elements you want written to the data file.
The files are created in the same folder as your .gsim simulation file. They have the same name as your .gsim file, except the extension is .txt. In Excel, choose file type txt and browse to the file. Choose deliminated, and choose the comma as your delimiter. Then it should open for you. If you want .xls, you can save it in Excel with file type xls.
Here are step-by-step instructions for creating the first simulation you linked to:
Open Gravity Simulator and pause the simulation
Open "fullsystem.gsim" which is in your "simulations" folder.
Objects > Delete
Delete all unwanted objects. Your article talks about the "14 main bodies". From their list I would delete Haley's comet as one of the 14 main bodies. You might also want to exclude Sedna, Eris and Pluto. If not, you might as well keep Ceres, Pallas, Vesta, and Juno, as they're more significant as Sedna.
Save your simulation. Create a new folder for it and give it a name.
The link you provide uses 2000 massless test particles. I'd suggest starting out with 200 until you are comfortable with creating simulations. Besides, 200 should be fine to show you their general distribution after a given time since they are massless and don't interact with each other. It says they are in circular orbits with inclinations distributed between 0 and 5 degrees. The article doesn't mention how they're distributed in distance. But looking at their animation, there don't seem to be any interior to Earth's orbit, and they seem to stretch out to Neptune. So let's just assume that they're evenly distributed between 1 and 30 AU.
Objects > Create Objects
Number of objects: 200
Semi-major axis: First hit the distribution button until the words "Start, End" appear under SMA. Make sure that AU is selected as your unit of distance. Enter 1,30
Inclination: Choose 2.5 degrees +/- 100%
Make sure the reference object is the Sun.
Give them a name such as "Asteroids"
Press Create
Under menu > Preferences, set the "Do Events" to 5 so your program doesn't seem non-responsive due the high number of objects. Also set the Graphics Updates to 50 to speed things up.
Save the simulation. Give it a different name than before in case you need to start over.
Unpause and watch.
To hold Jupiter still like they have in your article, use menu View > Rotating Frame Adjustment. Choose Jupiter. This gives you approximately the right period for the rotating frame. Experiment to come up with a better value. Hit "Calibrate" and click on Jupiter. Return a few minutes later and click on Jupiter again. Gravity Simulator will then compensate for Jupiter's drift.
To make the asteroids appear different colors depending on whether they're above or below the ecliptic, menu Objects > Edit Objects. Select each asteroid and put an asterick after its name and hit "Apply". I don't have an automated way to do this, sorry, so you'll just have to spend a few minutes and do them one at a time. Any object with * as the last character of its name appears red when below the ecliptic.
One more change I would make is to use Earth Barycenter rather than the Earth and the Moon. With the Moon orbiting the Earth, this sets the maximum step size you can use, preventing you from taking huge time steps like the 3 days they use in your link. Even so, I'd keep the time step to 16K seconds or less.
Following my above instructions, I just made one for you. You can get it here:
http://orbitsimulator.com/gravity/simulations/frederico.gsim At a timestep of 16384, it does about 6 years per minute, or about 27 hours to do 10000 years, so you'll want to run this thing over night, save it, and run it again the next night or any time your computer is free. You can speed things up a bit by pressing the P button on the Graphics Options interface. This disables the graphing.