[gmx-users] Protein-surface interaction during flow

[Kamps, M.]

Dear GMX users,

I am trying to simulate a flow of protein over and along a surface
structure. To do this, I have a box which is very long in its x
direction, relatively small in its y direction and its z dimension is
limited by an artificially created surface. These proteins will move
in the positive x direction, starting at around x=0, and move towards
the surface structure. At this point the protein will either pass
along the structure, or adhere to it through LJ/Coulomb interactions.
There will also be interactions between the (many) proteins flowing.
Essentially, I’m trying to create a flow.

However, I’m unsure on how to do this. If I set the proteins as a
acc-grps, they will continue to accelerate even after they have
adhered to the surface, essentially pulling them off. Is there a way
to set acc-grps for a specific amount of time or distance? After which
their velocities will guide them towards the surface structure? Or can
I give these proteins a starting velocity after which they just flow?
Any ideas?

Mark