Internal dynamics of biomolecules is often related to their biological function. In order to investigate the dynamics of proteins and nucleic acids we apply molecular dynamics simulations. Since we are interested both in local and global flexibility, we use different approximations of the molecules; from all-atom representation in explicit solvent to simplified coarse-grained models. All-atom molecular dynamics simulations are often too time consuming and computationally demanding to routinely achieve microsecond time scales for systems larger than 100 000 atoms. On the other hand, the coarse-grained representations are often sufficient to capture global collective dynamics on much longer spatial and temporal scales. However, due to reduction of the degrees of freedom, coarse-grained approaches typically require parameterizations of the potential energy function (force field).

I will present examples of applications of molecular dynamics simulations to proteins and nucleic acids and our efforts to design an automatic parametrization procedure for the coarse-grained model force fields.