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Before you design a geometry and simulate your experiment, you need to understand the basic concepts in Geant4. Most people will follow examples already implemented as their start up point. However, modifying examples without understanding the core of the geant4 engine will not get you anywhere.
First, one needs to have a background in C++ and OOP. There are lots of guides on internet if you don't have too much experience in this domain. Try:
Then you have to read and familiarized with the Geant4 engine BEFORE you change any sample code. The guide I am referring to:
You will need to familiarized with some important concepts. I would like to highlight:
[!!!] Every time you change your source code, or an example source code, you will need to re-build your application (your code). This is very important so to be able to see any changes in the output.
 The geometry: The universe you are simulating
 Physics list: The physics you want to use. You need to discover which physics list fits your application/purpose.
 The particle generator: How your particle of interest is produced. These particles will interact in your previous defined geometry and these interactions are governed by the physics you have chosen.
The last part is to collect data of interest and this could be easy or challenging depending on you. You could use objects provided by Geant4 developers or you could build your own.
After you review the application developer's guide, then you can go back to post
And work your application from and existing example. These is how most people start working and becoming familiar with geant4 environment.
Good luck with your application!