bioactive glasses are widely employed in repair and treatment of bone defects and also as an appropriate replacement for the ossicles in middle ear owing to their bonding ability to hard and soft tissues. In this research, the molecular dynamics package (GROMACS) was used to study the structure of bioactive glass synthesized by sol-gel method. To create related hydroxyl groups, the bioactive glass system was modeled. Then, a thermal cycle at temperature of 298-923 K with a constant rate was applied to the studied system and several parameters such as the internal structure, penetration coefficient, density and molecular weight, number of hydrogen bonding, bond length and bond angles were evaluated. Finally, the radial distribution functions were analyzed to study the structure of the bioactive glass, and the effect of the synthesis method on the bioactive glasses was also determined. The evaluation of the molecules density and simulation results of the bond angles and lengths indicated that materials are tend to be placed in the optimal condition and sustainable system. Due to the higher molecular weight of P₂O₅ and its lesser movement throughout the box, SiO₂ and CaO species played more important role in the uniform distribution of materials through the system. By determining the diffusion coefficient and molecules distribution via radial distribution function method in the simulation box, it was concluded that the system components had a fairly uniform distribution and there was an acceptable and logical distance between atoms in almost every molecule