The topic presented in this research is the calibration of small-scale parameters of non-classical continuum theories such as nonlocal strain gradient theory, strain gradient theory, stress-driven nonlocal elasticity, and strain-driven nonlocal elasticity. Governing equations of vibrational behavior of circular nanoplate and associated boundary conditions for each method derived using Hamilton's principle. Obtained governing differential equations from non-classical methods were solved using the general differential quadrature rule (GDQR). Then, the first natural frequencies for different radiuses and different size parameters were obtained. On the other hand, the first natural frequencies of circular nanoplates are calculated using molecular dynamics simulation based on AIREBO and Tersoff potentials for different radiuses. Fast Fourier transform (FFT) was utilized to calculate natural frequencies based on the molecular dynamics simulation. Using the accurate size parameter is an important point in the application of non-classical continuum theories. To obtain the size parameters related to different non-classical methods, the results of molecular dynamics compared to those of nan-classical methods and simulated annealing (SA) algorithm optimization technique was utilized. Results show that stress-driven nonlocal, strain-driven nonlocal, and strain gradient methods cannot predict the behavior predicted by molecular dynamics for all ranges of radius. In other words, the responses of these three methods for any value of the size parameters (in some interval radius) and results of the molecular dynamics method are not equal for a few numbers of studied radii. In contrast to these three methods, the nonlocal strain gradient method predicts the results obtained by molecular dynamics well for all radii. The results of this paper are very useful for researchers in the field of non-classical continuum mechanics.