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>>In my case, vibrating motors have their own self-weight and distribution mass over at point A. Are these two factors will affect the mode shapes and natural frequency?
Of course they do. Natural frequency is influenced by mass distribution and stiffness distribution. On the contrary, the fact that they are "vibrating", this has no influence on the natural frequency. Think of the natural frequency, as the word says, of a "property" of a certain structure, constrained in a certain way. Natural frequencies and modes are like a fingerprint of a structure. So be sure to put every significant mass in the model, in the appropriate position, either with point masses or with elements having the right density.
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>>Another doubt is, I am using two exciters, so the excitation frequency is double the value ( 2x 16 - 32 Hz) or Not?
It seems to me that you still mix the two concepts of free and forced vibration. For a natural frequencies (eigenfrequency) analysis, there is no excitation at all. Your structure, including the masses of the motors, will have the same natural frequencies if the motors vibrate or not. The motors will have to be represented as concentrated or distributed masses, that is all.
When you will have obtained a plausible set of natural frequencies and modes, you can make a step forward and ask yourself: ok, let's see, now I know that (e.g.) I have the smallest natural frequency at, say, 20.3 Hz. What will happen when the motors excity my structure? This is another type of analysis, this is an harmonic analysis. The answer will require an accurate input of the damping of the structure (low damping ---> high vibration). I will leave to some other user or ANSYS employee to answer how you can input two excitation points, because I never did this. Consider that probably the two excitation will not be in phase.
>>Totally what are the inputs I should apply to get correct natural frequency modes.
again: accurate distribution of the mass (center of gravity for the concentrated masses, correct density for the rest) + correct representation of constraints (be careful to constrain in the exact way the system is constrained in reality, consider that e.g. a bolted connection is not perfectly stiff and so on) + correct represenation fo the stiffness (E-module, all springs correctly represented, other stiffnesses). The excitation has nothing at all to do with natural frequency, they are called so because they are free.