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Background: The knowledge of parameter estimation for interatomic potentials is useful in the computation of the vibrational structure of van der Waals molecules. Methods: On the estimation of the Generalized Morse and Classical Lennard-Jones potential energy functions, complex conjugates eigenvalues may be obtained. Different approaches can be used to solve this resulting problem. A method that uses the objective least squares function method to estimate parameters of the interatomic potentials is employed. Results: Numerical simulation of the systems using metal atoms yields complex conjugates eigenvalues at some initial point. Conclusion: Other approaches of solving the complex conjugates eigenvalues problem are discussed comprehensively.