Many technologically important materials are used in amorphous form, and a fundamental understanding of their structure is crucial for optimization of their performance. Due to the disordered nature of amorphous materials, experimental structural characterization is challenging. Computational techniques such as ab initio molecular dynamics simulations have been widely used to reveal atomistic insights into the structural characteristics of amorphous materials. The simulated melt-quench process is typically used to generate the amorphous structure. Such generated structures contain varying amounts of defects due to differences in system sizes and simulation history. Consequently, reported structures for amorphous materials are subject to substantial variations and inconsistencies. Using silicon dioxide (SiO2) as a model system, the effects of simulation history on the structural characteristics of amorphous SiO2 have been studied. By manipulating simulation parameters such as time, temperature, and thermodynamic ensemble, this research examines which conditions eliminate the most defects in an amorphous structure through a statistical analysis. The optimal parameters for generating high-quality, defect-free amorphous SiO2 structures were proposed. The same protocol is expected to be applicable to other materials, thus advancing the study of amorphous materials by providing a reliable computational protocol for producing amorphous structures with minimal defects.