The deform option is not suited for shear flow
The deform option in mdrun gives and constant velocity to box vectors and scales coordinates at each step to follow the box deformation. This works acceptably in case the goal is to see some disruption after slow deformation. However for a shear flow setup the following is needed
- no coordinate scaling
- correction of the particle velocities of atoms when they are reset along periodic vectors
- substract the flow profile when computing the kinetic energy; problematic as a reference location is needed
- grompp should have the option to initialize the flow given given the deform matrix
This setup should also work fine for the "disruption" case, so we should do this by default.
Edited by Berk Hess