Shear simulations#

A common type of non-equilibrium simulations in fluid dynamics and rheology are shearing simulations. These are non-equilibrium simulations where work is performed on the simulation system to achieve a shear flow. This can be used to compute viscosities and friction and to study the effect of shear stress on conformations. In GROMACS there are four different ways to achieve shear flow.

Groups of atoms can be given a constant acceleration, which is effectively a mass-weighted force. This will cause such groups to move with respect to the rest of the system. Care needs to be taken to control the velocity of the center of mass of the system. Normal center of mass motion removal can not be used, as that would affect the flow in the system.

As GROMACS supports general triclinic unit-cell shapes, the unit cell can be deformed to set up a shear flow. This can be achieved either by deforming the unit cell directly using the deform option in the mdp file, or this can be driven by applying an off-diagonal stress through pressure coupling. In the former case, one can measure the viscosity through the stress, in the latter case through measuring the shear rate. Note that the with the deform option, gmx mdrun corrects the velocities of particles that are moved by a periodic vector for the difference in flow velocity. Such a correction is not applied when using a stress to generate a flow.

For measuring the viscosity of simple liquids one can use a cosine-shaped acceleration profile, which can be specified using the cos-acceleration option in the mdp file. As the unit-cell does not deform, this avoids some complications of the other methods. The viscosity is computed on the fly and reported in the energy file.

And finally, there is the case where one wants to study the effect of walls on the flow. In particular, structured walls are of interest, consisting of atoms that can be of any kind. In this case one wants to have walls on two sides of the system, typically in the xy-plane close to z=0 and the box height. The flow is then driven by moving the walls at constant speed by using a constant force. A constant force can be achieved by use of acceleration groups, but that will not allow position restraining atoms in the walls along the direction of the shear, which is needed for some types of walls. For the case of walls where (part of) the atoms are position restrained, a constant speed can be set by using the free-energy lambda-coupling code. To achieve this, you need to supply a second, B-state, position restraint file with the -r option of gmx grompp. If you shift the coordinates in this file by 1 nm in the direction of shear, you can set the speed of the walls with the delta-lambda option in the mdp file. Note that this makes lambda increase proportionally with simulation time. There is no limit on magnitude of lambda and periodic shifts of walls are handled correctly. When the position restraint coordinates are shifted by 1 nm, the force on the walls is given directly by \(dV/d\lambda\).

A Poiseuille flow is a popular setup in experiments. Unfortunately this is difficult to achieve in simulations. The best would be to, as in experiment, apply a pressure difference over (part of) the simulation box. But that is not easy to set up. One can accelerate all liquid atoms, but this does not guarantee that atoms that interact directly with the wall experience the same forces as they would in an experiment. A slightly better setup would be accelerating only the atoms in the middle of the flow, but spatially defined acceleration groups are currently not supported in GROMACS.