Torque constraints for modeling the behavior of rigid and semirigid macromolecules

Abstract

This work investigates the rotational dynamics of rigid and partially flexible macromolecules in solution by means of Brownian dynamics simulation techniques. In a previous study by Diaz et al. [J. Chem. Phys. 87, 6021 (1987)] on the rotational correlation functions of rigid models, the effect on rotational dynamics from pure rotations of the model’s elements has been neglected due to the difficulty of introducing rotational constraints in the simulations. We present expressions for rotational constraints in a rigid dimer system, which makes it possible to completely describe the translational, rotational, and coupled translational–rotational motions for interacting spherical Brownian particles by employing the generalized algorithm of Dickinson et al. [J. Chem. Soc. Faraday Trans. 2 81, 591 (1985)]. Theoretical studies indicate, and our simulation calculations confirm, that the pure rotational effects are appreciable. The torque constraint expressions are verified by comparison of the simulation results to the exact analytical results for the rigid dimer system. The torque constraint expressions also allow us to examine the effects of flexibility on the rotational correlation functions for a dimer system.