Hi GROMACS community,
I’m looking for a way to keep waters and ions out of a ligand binding pocket during MD simulation.
The protein I’m interested in is a membrane protein, whose ligand binding pocket is filled with several random waters in the apo form.
I want to see what happens if I intentionally keep the waters (and ions) out of the pocket during the simulation, and discuss the roles of the waters in the pocket.
I hoped to be able to do something like the following, but I couldn’t find how can I set up such a simulation so far. (I’m a newbie to MD simulation.)
- Calculate the CoG of the binding pocket.
- Apply repulsive forces to waters and ions within certain distance from the CoG. (By something like the flat-bottomed harmonic potential.)
- But don’t want to apply any counteracting forces on the protein side.
- The CoG must be periodically updated, because the protein is not confined its position in the simulation box.
My question is, how would you go about doing such a simulation? Is it possible with gromacs?
I appreciate any comments from the community.
Thanks in advance