In order to determine the distribution of strain inside hemispherical InAs quantum dots (QDs) embedded in GaAs, molecular dynamics (MD) simulation is applied. Taking into account the distribution of strain, the conduction band minimum (CBM) profile was calculated, We found that the CBM inside the QD is significantly higher than that for the bulk InAs. The electrons tend to be confined in the potential well that exists at the InAs/GaAs interface. As the capping layer thickness of the QD increases, the strain felt by the QD increases but the depth of the potential well decreases, reducing the quantum confinement effect. We believe that MD simulation is a powerful tool that can be used to investigate the distribution of strain in QDs with different compositions, sizes and shapes. Applying the eight-band k.p perturbation Hamiltonian to the simulation results can give a better picture of the real electronic structure of these QDs.