Acceleration vs. mass (kg) graph

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If in an acceleration vs. mass (kg) graph (where the x-axis reads (1/m1+m2), the inverse of the sum of masses), the best fit does interesect with the origin because if x = zero, or (1/m1+m2) = o, the final solution is unreal since it is mathematically incorrect to divide one by zero.

Likewise, in an acceleration vs. differences of masses, best interesects with origin since when m1-m2=0, acceleration, as as result, equals to zero.

Finally, would it be correct to stay that the y interest of an acceleration vs. mass graph represents the acceleration of the system when 0 masses are involved, or does it repersent the gravitational mass (resistance)?
 
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If you plot the inverse mass then the y intercept correspond to infinite mass, which can't be moved with a finite force. No gravity involved (unless it's providing the force being studied).
 
It looks like you are describing an Atwood machine experiment in which the acceleration is $$a=\frac{m_2-m_1}{m_2+m_1}g=\frac{\Delta M}{M}g.$$The usual procedure is to keep the total mass ##M## constant and move some mass from one side to the other to vary ##\Delta M##. Then a plot of acceleration vs. ##\Delta M## has slope ##g/M## from which one can deduce the acceleration of gravity.

This is the the case when the pulley is massless which never happens. A real pulley with moment of inertia ##I## and radius ##R## has effective mass ##m_{eff}=I/R^2## in which case the measured acceleration is $$a=\frac{\Delta M}{M+m_{eff}}g\approx \frac{\Delta M}{M}\left(1-\frac{m_{eff}}{M}\right)g.$$In the non-ideal pulley case, there is an intercept which can be used to find the effective mass.