  We simulated two particle-based fluid models, namely multiparticle collision
dynamics and dissipative particle dynamics, under shear using reverse
nonequilibrium simulations (RNES). In cubic periodic simulation boxes, the
expected shear flow profile for a Newtonian fluid developed, consistent with
the fluid viscosities. However, unexpected secondary flows along the shear
gradient formed when the simulation box was elongated in the flow direction.
The standard shear flow profile was obtained when the simulation box was longer
in the shear-gradient dimension than the flow dimension, while the secondary
flows were always present when the flow dimension was at least 25% larger than
the shear-gradient dimension. The secondary flows satisfy the boundary
conditions imposed by the RNES and have a lower rate of viscous dissipation in
the fluid than the corresponding unidirectional flows. This work highlights a
previously unappreciated limitation of RNES for generating shear flow in
simulation boxes that are elongated in the flow dimension, an important
consideration when applying RNES to complex fluids like polymer solutions.
