ROTATIONAL DYNAMICS OF LARGE MOLECULES

We describe a set of computer algorithms to solve Newton's equations of motion for large molecules (biopolymers) directly in terms of generalized coordinates (the bond rotation angles). The programme package is designed to deal both with equilibrium and non-equilibrium situations. The effect of solvent is simulated by the explicit inclusion of friction terms. The main features required to solve the equations are a coding scheme to represent the topology of the molecule, a rotation algorithm, an efficient method to compute the torques, and a flexible integration scheme that is stable for the wide range of time scales characteristic of polymer systems. The effectiveness of our approach is demonstrated on a biologically important molecule, with nine degrees of freedom. Generalizations and extensions are discussed. © 1979.