Dimensionless variables of the differential equation
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MATLAB cannot "make" a solution dimensionless, since again, MATLAB does not understand units on variables. (With the exception of computations done with the symbolic toolbox as has been pointed out, and since you are using ODE45, that does not apply. It is also why I did not mention that capability.) Only you can insure something is dimensionless, which requires that you understand the formulation of your equations, and those equations were properly rendered dimensionless when you created them. It seems the part that is lacking is your understanding here.
MATLAB is just a tool. It does what you tell it to do, nothing more and nothing less. And it you tell it to do something physically meaningless, it will still proceed and do as it is told. The result will of course, be meaningless. But that is not the fault of MATLAB, but the user.
I'm starting to see what you did wrong. Almost enough for my response here to qualify as an answer, but not really.
You divided the equations by length, thinking this makes the length a dimensionless variable. But force has units of mass*distance/time^2. (For example, a common unit of force might be represented as Kg*M/sec^2.)
It is not at all clear what you did to make force dimensionless. Dividing by length does not result in a dimensionless force.
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