One of the great successes in the field of engineering, whether aeronautical, civil, or mechanical, was the development of the Finite Element Method, thanks to which problems of solid mechanics, fluids and even fluid-structure interaction can be solved with great precision. In its origins, the method was applied mainly to macroscale problems, while at the atomic scale the use of Molecular Dynamics has been the more usual way. As an alternative to the Molecular Dynamics method, we propose a new formulation that allows obtaining the stiffness matrices directly from the force-field, without resorting to simplifications other than those used in its parameterization. The formulation allows both first order analysis, linear instability, and geometric nonlinear analysis. In the case of first-order analysis, we applied this formulation to the vibrational analysis of different simple molecules [1,2], also including the parameterization of its force constants [2]. In turn, it has been applied to the study of the mechanical behavior of protein structures, such as coronavirus spikes or viral capsids. The formulation has also allowed the study of linear buckling of structures such as carbon nanotubes and graphene sheets, allowing the development of equivalent continuous models of increasing interest in materials science [3]. Moreover, the inclusion of geometrical nonlinearities has allowed the study of nonlinear phenomena such as buckling in nanotubes both as monolayer and multilayer or in fullerenes. REFERENCES [1] F. Navarrina, Matrix Calculation of Molecular Structures, Technical Report, GMNI (2021). [2] A. Fernández San Miguel, Dynamic Analysis of Molecular Structures, Technical Report, GMNI (2021). [3] Ellad B. Tamor & Ronald E. Miller, Modeling Materials: Continuum, Atomistic and Multiscale Techniques, Cambridge University Press, (2011).