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I am building my own autonomous quadcopter. I wish to simulate it using V-REP/Gazebo in order to tune the flight controller. I see that there are inbuilt models but they have properties(physical dimensions and mass among others) very different from the one I am building.
1) Can I modify these models so that it can simulate my drone? Is it enough to change the geometry, mass and inertias to make it work?
2) Do I have to deal with the physics and aerodynamics? Or do these simulators take care of it? If not what is there primary purpose of these simulators?
3) What is the process in general of simulating your hardware(in this case the quadcopter) in these simulators?

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I have never used it ,because I have always dealt with custom simulators but I know others have had success with the RotorS simulator.

Answers to your questions:

1) Can I modify these models so that it can simulate my drone? Is it enough to change the geometry, mass and inertias to make it work?

Kind of. You could just take one of their existing models, and change the mass and geometry. However, you would be using their hardware models for the motors which will give you slightly different results.

2) Do I have to deal with the physics and aerodynamics? Or do these simulators take care of it? If not what is there primary purpose of these simulators?

The simulator will do the basic dynamics, and physics. For aerodynamics they usually do take care of things like rotor drag, and RotorS even has the capability of adding a wind field.

3) What is the process in general of simulating your hardware(in this case the quadcopter) in these simulators?

Don't understand exactly what you mean here. You can simulate your hardware in regards to setting accurate values for your motors, and inertial sensors. You can also setup hardware in the loop with the pixhawk if you want to test your system.

To end it I would also say the purpose of these simulators is more to test the validity of your algorithms (mostly control, and some path planning) rather than to tune your flight controller. To tune something you want an accurate physical model, which is hard to come by in simulation. It either requires you generally doing a lot of experiments to get accurate values, or some kind of System ID algorithm.

In your case it sounds like some kind of autotuning algorithm may be better as found on the pixhawk.

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