A first principle molecular dynamics (MD) simulation study on the nonlinear excitations in a quasi-localized state of a Yukawa system is presented to validate the findings of the nonlinear quasi-localized charge approximation (QLCA) model. Unlike solids or gases, quasi-localized states lack certain simplifying features, such as the ability to assume a fixed shape or volume, and they combine large displacements with strong interactions, further complicating the theoretical underpinnings of their behavior. In a recent paper [P. Kumar and D. Sharma, Physics of Plasmas 30 (2023)], the nonlinear QLCA model was applied to characterize the nonlinear excitations in a quasi-localized state of a Yukawa system, as existing continuum models have shown limited success in this regime. The simulation data presented with the screening and coupling parameters show a close agreement with the QLCA model findings. The MD simulations validate the prediction made by the QLCA model that the properties of a soliton remain unaffected by variations in the coupling parameter. The prediction made by QLCA regarding the formation of multiple solitons at higher screening parameter values has also been confirmed by the MD simulation data. The possibility of the formation of rarefactive solitons at relatively high screening parameter values within the QLCA model is also discussed.