We present a systematic study of the effects due to initial condition fluctuations in systems formed by heavy-ion collisions using the hydrodynamical simulation code NeXSPheRIO. The study was based on a sample of events generated simulating Au+Au collisions at center of mass energy of 200 GeV per nucleon pair with impact parameter ranging from most central to peripheral collisions. The capability of the NeXSPheRIO code to control and save the initial condition (IC) as well as the final state particles after the 3D hydrodynamical evolution allows for the investigation of the sensitivity of the experimental observables to the characteristics of the early IC. Comparisons of results from simulated events generated using fluctuating initial conditions and smooth initial condition are presented for the experimental observable elliptic flow parameter ($v_2$) as a function of the transverse momentum, $p_t$, and centrality. We compare $v_2$ values estimated using different methods, and how each method responds to effects of fluctuations in the initial condition. Finally, we quantify the flow fluctuations and compare to the fluctuations of the initial eccentricity of the energy density distribution in the transverse plane.
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