The variability of molecular vibrations and low terahertz spectra of biological molecules depending on the three-dimensional structure of molecular clusters, chemical bonding, and molecular concentration in the surrounding media is studied using computer simulations. The resonant terahertz spectra of biological molecules and their associations are described within the framework of molecular mechanics using an all-atom molecular mechanical force field for proteins and nucleic acids. Both the absolute values of absorption coefficients and their spectral properties are considered for murein-lipoprotein and thioredoxin of E. coil and models of bacterial DNAs using energy minimization and molecular dynamics. The obtained results indicate that structural changes introduced by chemical reactions and molecule associations can strongly affect terahertz spectra, causing significant changes in absorption peak intensities and shifts in peak positions. Terahertz light absorption intensities of studied proteins are predicted to be strongly affected by solvents.