Self-assembled ordered structures composed of block copolymers are simulated by molecular dynamics under stress-free conditions and under shear. We address several methodological points. The system must be allowed to adjust its size to accommodate natural periods of self-assembled structures. In addition, these structures need to be capable of rotating freely under shear. An examination of the diffusion of polymer molecules in the lamellar phase reveals subdiffusion along translationally invariant directions between the ballistic and diffusive regime. The diffused distance d increases with time t as d cc t(1/3). We also examine the possibility of mapping structures such as cylindrical phases onto particle-field types of models. Using measurements of the wavevector-dependent dynamic matrix, we show that this cannot be done with only two-body potentials. We then examine the molecular origin of shear alignment of lamellar phases. Lamellae oriented parallel to the shear direction become unstable at high shear rates when the major axis of the tensor of gyration of individual polymers forms an average angle of 45 degrees with the lamellae. This instability can be understood in analogy to similar transitions in liquid crystals. (c) 2005 Wiley Periodicals, Inc.