A Free Energy Approach to the Torsion Dynamics of Macromolecules

Based on the concept of free energy, we give a Hamiltonian formulation for the torsion dynamics of macromolecules. The appropriate reaction coordinates for the free energy calculations are deened in terms of soft constraints as introduced in 3] and 14]. We consider a few simpliications that allow one to calculate the free energy analytically and to write the corresponding equations of motion as a constrained Hamiltonian system. We also discuss a possible stochastic embedding of the reduced dynamics by means of a generalized Langevin approach.