Abstract <p>The analysis of multi-atomic systems from the first principles is highly computationally intensive, therefore it requires the finding of integral degrees of freedom. We propose the usage of the lattice Abelian Higgs model for the study of protein structure and dynamics. At the first step we have introduced heterogeneous external electric field in this model and have shown how this field affected the tertiary protein structure. At the second step we found the form of external field corresponding to native protein structure with experimental accuracy. We believe that this approach will allow one to model protein dynamics depending on external conditions.</p>